title: Xyloglucan, TF13, biol rep 3

city: Ljubljana

first: Urška

last: Murovec

address: Jamnikarjeva 101

country: Slovenia

institute: Biotechnical Faculty

data_processing:
fastQC, Trimmomatic v0.39, BWA tool 0.7.17-r1188, FeatureCounts 2.0.0, R 4.1.2
Assembly: SPAdes genome assembler v3.15.3
Supplementary files format and content: raw counts for each sample

organism: Segatella bryantii

source_name: Segatella bryantii TF1-3

extract_protocol:
Strains were grown in liquid minimal or modified DSMZ medium 330 containing different substrates, until they reached OD value of 0.3-0.5. 1.5 mL of each triplicate was removed and immediately combined with 3 mL of RNAprotect bacteria reagent (Qiagen). RNA was purified using RNeasy Mini Kit (Qiagen) with the on-column DNase treatment. The quantity of the isolated RNA was determined using Spark 10M multifunctional microplate reader with Quant-iTTM RNA Assay Kit (Thermo Scientific).
Illumina stranded TruSeq RNA library incl bacterial ribodepletion or NEBNext Ultra Directional RNA library prep kit

value: liquid culture

tag: treatment

value: Xyloglucan


title: Starch, TF13, biol rep 2

status: Public on May 08 2024

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: strain

tag: tissue

value: Starch


title: melanoma_FFPE_1 [20170815_Karen01_K01_01]

type: RNA

city: New York

first: Tiphaine

middle: Christiane

last: Martin

address: 1470 Madison Ave

department: Oncological Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute

hyb_protocol: 200 ng RNA was hybridized to a custom NanoString panel code set according to the recommendations of the manufacturer (NanoString Technologies, Inc., Seattle, Washington, USA).

scan_protocol: Following hybridization, the target-probe complexes were purified and immobilized on the nCounter prep station. Digital counts for each gene-specific target RNA were then acquired on the nCounter detection analyzer and normalized to account for differences in tissue mRNA quantity as well as slight differences in assay efficiency.

data_processing: The nSolver analysis software version 4.0 (NanoString Technologies) was used for extraction of raw digital counts of expression, checking the quality of the data, normalizing expression values using housekeeping genes, and generating heatmaps.

label: customized panel

organism: Homo sapiens

source_name: primary melanoma FFPE tissue

label_protocol: Specimens were labeled with decode assignment which was linked to tumor origin.

growth_protocol: This cohort includes human tissue obtained from FFPE (n=205), fresh frozen human tissue (n=24), and human cell lines (n=12).

extract_protocol: RNA was obtained from the FFPE human tissue samples using the RecoverAll Total Nucleic Acid Isolation kit. RNA was obtained from the fresh frozen human tissue samples using the Qiagen Rneasy kit. Cell lines were pelleted and RNA was harvested using the Qiagen Rneasy kit.

tag: gender

value: F

tag: age at diagnosis

tag: cohort

value: Sinai

tag: tnm

tag: stage at original diagnosis

value: IIA

tag: ajcc thickness

tag: breslow thickness

tag: ulceration

value: Absent

tag: os

tag: pfs

tag: dead or alive at last contact

value: Alive

tag: tag

value: primary cutaneous melanoma tissue


title: h26766_82_rv

city: St. Louis

first: Mathieu

last: Garand

state: MO

address: One Childrens Place Suite 6120

department: Surgery

institute: Washington University in St. Louis

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read
RNA-seq reads were aligned to GRCh38 (GENCODE 20) with STAR version 2.0.4b
A count of a per million threshold equivalents to ∼10 raw expression value
Filtered transcripts were then annotated to gene symbols using org.Hs.eg.db and org.Mm.eg.db
Assembly: GRCh38
Supplementary files format and content: .csv; matrix of raw counts, transcripts (ENSG ID) as rows and samples as columns

source_name: Heart Tissue

extract_protocol:
MagneSil® PMPs on the Promega Maxwell 16
SMARTer Ultra Low RNA kit (Takara-Clontech)

value: Heart Tissue

tag: disease

value: No Disease

tag: group

value: RV

tag: Sex

value: male

tag: gestational age


title: Rhamnogalacturonan, TF13, biol rep 2

tag: strain

tag: tissue

tag: treatment

value: Rhamnogalacturonan


title: h26766_82_lv

value: LV


title: Rhamnogalacturonan, TF13, biol rep 1


title: Rhamnogalacturonan, TF13, biol rep 3


title: 018_NR_4

city: Crawley

first: Jonathan

last: Chee

state: WA

address: M503, 35 Stirling Highway

country: Australia

institute: University of Western Australia

data_processing:
Agilent TapeStation for quality control of DNA integrity.
Paired-end (2 × 300 bp) high-throughput sequencing was performed using the Illumina MiSeq platform.
Data processing, aggregation of UMIs and alignment of CDR3 sequences to the IMGT/V-QUEST reference genome were performed using repertoire analysis software based on MIGEC and MiXCR pipelines. Only sequences with UMIs were aligned.
TCRβ clones (defined by the CDR3 amino acid sequence) were excluded if they were less than 8 or greater than 20 amino acids in length, included a stop codon or a frameshift.
Assembly: IMGT/V-QUEST reference genome
Supplementary files format and content: txt files
Supplementary files format and content: clonotype tables
Library strategy: TCR-seq

organism: Mus musculus

source_name: Tumour

extract_protocol:
Sorted cells were stored at -80C. RNA was extracted from frozen cells using the RNeasy Plus Micro Kit.
TCRβ amplicon libraries were generated with 5’Rapid Amplification of cDNA Ends (5’RACE) technology. RNA was transcribed to cDNA with a TCRβ constant region primer and a modified SMARTerIIA primer (Integrated DNA Technologies), with 9nt long unique molecular identifiers (UMI) added to individual TCRβ cDNA sequences. TCRβ locus was amplified by nested PCR with an additional TCRβ constant region primers, and a universal primer to SMARTerIIA, with the final PCR adding sequencing adaptors and barcodes to the TCRβ libraries. Products after each PCR were purified using AMPure XP AgenCourt Beads (Beckman Coulter).

treatment_protocol: Whole tumours were surgically excised from mice

value: BALB/c

value: Tumour

tag: cell type

value: RENCA

tag: timepoint

value: day  0


title: h26743_87_lv


title: Xyloglucan, TF13, biol rep 2

value: liquid culture

value: Xyloglucan


title: Pectic galactan, TF13, biol rep 3

value: Pectic galactan


title: Xyloglucan, TF13, biol rep 1


title: h26834_89_lv

value: female


title: Starch, TF13, biol rep 3

value: Starch


title: h26820_126_lv

value: HLHS


title: melanoma_FFPE_5 [20170815_Karen01_K09_09]

tag: gender

value: M

tag: age at diagnosis

tag: cohort

value: Sinai

tag: tnm

tag: stage at original diagnosis

value: IV

value: Present

value: Alive

value: primary cutaneous melanoma tissue


title: h26742_89_lv

value: Heart Tissue

value: No Disease

value: LV


title: Starch, TF13, biol rep 1


title: 049_RS_5

value: BALB/c

value: Tumour

value: RENCA


title: Pullulan, TF13, biol rep 3

value: liquid culture

value: Pullulan


title: 640_RS

value: day  6


title: h26743_87_rv

value: RV

value: male


title: Glucomannan, TF13, biol rep 2

value: Glucomannan


title: Homogalactuornan, TF13, biol rep 1

value: Homogalactuornan


title: Glucomannan, TF13, biol rep 3


title: Pullulan, TF13, biol rep 2


title: Pullulan, TF13, biol rep 1


title: 009_RS_3

value: day  0


title: 630_NR


title: Pectic galactan, TF13, biol rep 2

value: Pectic galactan


title: 005_RS_2


title: Pectic galactan, TF13, biol rep 1


title: h26742_89_rv

value: female


title: 003_RS_1


title: 051_NR_6


title: Homogalactuornan, TF13, biol rep 2


title: Homogalactuornan, TF13, biol rep 3


title: 633_RS


title: Glucomannan, TF13, biol rep 1


title: h26741_98_rv


title: h26741_98_lv


title: Glucose, TF13, biol rep 3

value: Glucose


title: JK4.2_2.1_T_R_4

value: day 13


title: 627_RS


title: h26733_88_lv

value: Heart Tissue

value: No Disease


title: h26733_88_rv


title: Glucose, TF13, min, biol rep 2


title: Glucose, TF13, biol rep 1


title: h26731_90_lv

value: LV


title: Glucose, TF13, min, biol rep 1


title: JK4.2_2.1_T_L_8

value: BALB/c

value: Tumour


title: Galactomannan, TF13, biol rep 1

value: liquid culture

value: Galactomannan


title: Glucose, TF13, biol rep 2


title: Galactomannan, TF13, biol rep 2


title: Glucose, TF13, min, biol rep 3


title: h26731_90_rv


title: JK4.2_2.1_T_L_4


title: h26720_90_rv


title: JK4.2_2.0_T_R_8


title: Beta-glucan, TF13, biol rep 3

value: Beta-glucan


title: Galactomannan, TF13, biol rep 3


title: h26720_90_lv


title: Beta-glucan, TF13, biol rep 2


title: Beta-glucan, TF13, biol rep 1


title: JK4.2_2.0_T_R_4


title: h26714_89_rv

value: RV


title: Beta-glucan, TF13, min, biol rep 2


title: Beta-glucan, TF13, min, biol rep 3


title: Beta-glucan, TF13, min, biol rep 1


title: h26714_89_lv


title: JK4.2_2.0_T_L_8


title: Arabinan, TF13, biol rep 3

value: Arabinan


title: Arabinan, TF13, biol rep 1


title: Arabinogalactan, TF13, biol rep 3

value: Arabinogalactan


title: JK4.2_2.0_T_L_4


title: SCZ_8D GPC

city: Rochester

first: Steven

last: Goldman

state: NY

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

description: RNA-seq, reanalysis of GSM2344524

data_processing:
The sequencing reads were pre-processed with fastq(Chen et al., 2018), aligned with STAR (Dobin et al., 2013) to the genome assembly GRCh38 (Flicek et al., 2014), and quantified with RSEM (Li and Dewey, 2011) using the ENSEMBL Homo sapiens version 95 annotation.
Genome_build: GRCh38
Supplementary_files_format_and_content: RawCounts
Supplementary_files_format_and_content: TPM

source_name: GPC induced from iPSC

growth_protocol: GPCs were generated from human induced pluripotent stem cells (iPSCs) using our previously described protocol (Wang et al., 2013, Windrem et al., 2017). Cells were harvested on the basis of the expression of the bipotential GPC surface marker CD140a or the astrocytic marker CD44.

extract_protocol: Glial cell populations where used in mRNA isolation by PolyA selection and mRNA sequencing analysis, utilizing the TruSeqRNA Library Prep Kit V2.

value: schizophrenia


title: Arabinan, TF13, biol rep 2


title: Arabinogalactan, TF13, biol rep 2


title: JK4.2_1.3_T_R_8


title: Arabinogalactan, TF13, biol rep 1


title: SCZ_8C GPC

description: RNA-seq, reanalysis of GSM2344523


title: JK4.2_1.3_T_R_4


title: JK4.2_1.3_T_L_8


title: SCZ_8A GPC

description: RNA-seq, reanalysis of GSM2344521


title: SCZ_51G GPC

description: RNA-seq, reanalysis of GSM2344520


title: SalmonellaExpression_Salmonella_withCaco2_andB_infantis_60mins_Rep1

city: Davis

first: Bart

last: Weimer

state: CA

address: 1 Shields Ave

institute: UC Davis

hyb_protocol: An aliquot of 500ng for pure culture and 2,000ng for coculture was hybridized onto the respective chips.

scan_protocol: 3,000 GeneChip Scanner with Autoloader (Affymetrix). All samples were proceesed according to Affymetrix protocols.

data_processing: Raw data (.cel files) were background corrected, quantile normalized and summarized using RMA (Irizarry et al., 2003).

label: biotin

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

source_name: Stationary Salmonella enterica sv. Typhimurium expression after 60 mins incubation with Bifidobacterium infantis and Caco2 cells

label_protocol: Fragmented cDNA was labeled using GeneChip DNA Labeling reagent (Affymetrix) and Terminal Transferase enzyme (NEB) as per manufacturers' reccomendation by using 2uL GeneChip labeling reagent and 3uL TdT/ug cDNA at 37˚C for 60min.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: ATCC


title: JK4.2_1.1_T_R_4


title: SCZ_51F GPC

description: RNA-seq, reanalysis of GSM2344519


title: JK4.2_1.3_T_L_4


title: SCZ_51E GPC

description: RNA-seq, reanalysis of GSM2344518


title: JK4.2_1.1_T_R_8


title: Co2880-IT2

city: Göttingen

first: Ting

last: Sun

state: Germany (DEU)

address: Hermann-Rein-Straße 3

department: Neurogenetics

country: Germany

institute: Max Planck Institute for Multidisciplinary Sciencesi

data_processing:
Data were demultiplexed using bcl2fastq and further controlled for sequencing quality using FastQC (Galaxy Version 0.72).
After verifying data quality, alignment was performed against reference genome Mmul10. Raw count profiles were extracted from aligned bam files using featureCounts, and normalized TPM values were calculated.
Assembly: Mmul_10
Supplementary files format and content: comma-delimited matrix include raw counts for RNA-seq results from both replicates
Supplementary files format and content: comma-delimited matrix include TPM normalized counts for RNA-seq results from both replicates

organism: Macaca mulatta

source_name: Cortex

growth_protocol: Tissue samples for trigeminal ganglia, brain cortex and hippocampus were obtained from two male animals sacrificed at age of 6 (animal 2817) and 7 (animal 2880) years for reasons unrelated to this project. Tissue samples were chopped into small (1 mm) pieces, transferred to separate Eppendorf tubes und incubated in 1 mL PBS containing 5 mg Collagenase IV. Samples were incubated for 1-3 hours at 37°C and 800 rpm in a thermomixer. After centrifugation for 5 min at 300 x g, cells were resuspended in medium and seeded separately into 6-well plates in a total volume of 3 mL/well. For neuronal tissue derived cells, DMEM/F12 was used as medium. All media were supplemented with 10% FCS and penicillin, streptomycin, gentamycin, nystatin and amphotericin B.

extract_protocol:
For RNA-isolation, selected MamuCo2888-gr and MamuCo2880-IT cells were seeded in 12-well plates in duplicate samples. After 24 h, total cellular RNA was extracted using the TRIZOL reagent (Ambion, Austin, TX, USA) following the manufacturer’s instructions.
Extracted total RNA was subjected to 50 bp single-end (for gr cell line) abd 50bp pair-end (for IT cell line) bulk RNA sequencing (Illumina HiSeq 4000).
50bp single-end (gr cell) and pair-end (IT cell) bulk RNA-seq

treatment_protocol: After few passages, cells were transduced with lentiviruses expressing human TERT, SV40 large T, or a mixture of genes shown to immortalize cells. To avoid TRIM5α-mediated restriction of HIV-based vectors we used a modified lentiviral system, which included a chimeric SIV/HIV-Gag protein. For the sequencing protocol, cells underwent selection with puromycin or hygromycin resistant after transduction with a gene mixture (termed “gr”).

value: Cortex

tag: age

value: 7 years

tag: genotype

value: WT

value: male


title: SCZ_8B GPC

description: RNA-seq, reanalysis of GSM2344522

tag: disease


title: SCZ_51C GPC

description: RNA-seq, reanalysis of GSM2344517


title: JK4.2_1.1_T_L_8

value: day 13


title: JK4.2_1.1_T_L_4


title: JKB201_2_4_3

source_name: Peripheral blood

value: Peripheral blood

value: day 3


title: SalmonellaExpression_SalmonellaAlone_60mins_Rep2

source_name: Stationary Salmonella enterica sv. Typhimurium expression after 60 mins incubation in DMEM

value: 60 mins incubation in DMEM


title: SalmonellaExpression_SalmonellaAlone_120mins_Rep2

source_name: Stationary Salmonella enterica sv. Typhimurium expression after 120 mins incubation in DMEM

value: 120 mins incubation in DMEM


title: SCZ_51B GPC

description: RNA-seq, reanalysis of GSM2310231


title: SalmonellaExpression_SalmonellaAlone_60mins_Rep1


title: H9-PE, Illumina, rep 2

city: Ann Arbor

first: Kin Fai

last: Au

state: MI

address: 100 Washtenaw Avenue

department: Department of Computational Medicine and Bioinformatics

institute: University of Michigan

data_processing:
For ONT long-read RNA-seq, only the long reads with a quality score (qscore ≥7, passed reads) are used for our study, and these passed reads are uploaded to NCBI GEO.  For Illumina short-read RNA-seq, sequencing adapters are trimmed by Cutadapt (v1.8.1)  with the parameter “-q 20,20 -m 20 --max-n 0.01 --trim-n”.
ReDD (v1.0.0) with sample-specific model is run separately on the ONT direct RNA seq data to obtain the A-to-I editing sites and editing level.
REDItools2 (v2.0.0) is run on the Illumina RNA-seq data to obtain the A-to-I editing sites and editing level.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files included the A-to-I editing sites and the editing level of the sites by ReDD.
Supplementary files format and content: Tab-delimited text files included the A-to-I editing sites and the editing level of the sites by REDItools2.

molecule: polyA RNA

growth_protocol: Definitive endoderm (DE) and pharyngeal endoderm (PE), and primordial germ cell-like cells (PGC) (reference: PMID: 37709760) are differentiated from human ESC (H1-hESC cell line), respectively. See the details in the manuscripts: (1)  DOI: https://doi.org/10.1101/2022.06.26.497457 (from ESC to DE and PE); and (2) PMID: 37709760 (from ESC to PGC).

extract_protocol:
Total RNA is extracted by TRIzol Reagent (Thermo Fisher Scientific), followed by polyA+ RNA enrichment using the Dynabeads mRNA Purification Kit (Thermo Fisher Scientific).
For H1-ESC, H1-PE, H1-DE, H1-PGC,H9-hESC,H9-PE,H9-DE and HEK293T, ONT sequencing libraries are prepared using the SQK-DCS109 Kit for direct RNA sequencing (dRNA-ONT). ONT sequencing is conducted using MiniON/GridION flow cells with R9.4.1 chemistry, with real-time base calling performed by the Guppy software. The library preparation and sequencing of Illumina RNA-seq data are conducted by Novogene company.

tag: cell line

value: H9-hESC derived pharyngeal endoderm


title: SCZ_51A GPC

description: RNA-seq, reanalysis of GSM2310230


title: SalmonellaExpression_SalmonellaAlone_120mins_Rep1


title: H9-DE, Illumina, rep 2

value: H9-hESC derived definitive endoderm


title: SalmonellaExpression_Salmonella_withCaco2_andB_infantis_120mins_Rep1

source_name: Stationary Salmonella enterica sv. Typhimurium expression after 120 mins incubation with Bifidobacterium infantis and Caco2 cells


title: SalmonellaExpression_Salmonella_withCaco2_60mins_Rep1

source_name: Stationary Salmonella enterica sv. Typhimurium expression after 60 mins incubation with Caco2 cells

value: 60 mins incubation with Caco2 cells


title: SalmonellaExpression_Salmonella_withCaco2_60mins_Rep2


title: SalmonellaExpression_Salmonella_withCaco2_andB_infantis_60mins_Rep2

value: 60 mins incubation with Bifidobacterium infantis and Caco2 cells


title: SalmonellaExpression_Salmonella_withCaco2_andB_infantis_120mins_Rep2

value: 120 mins incubation with Bifidobacterium infantis and Caco2 cells


title: H9-PE, Illumina, rep 1


title: H9-DE, Illumina, rep 3


title: H9-hESC, Illumina, rep 3

value: H9 human embryonic stem cells


title: JKB201_2_4_2

value: BALB/c

value: day 2


title: JKB201_2_4_1

value: day 1


title: JKB201_2_0_3


title: SCZ_29B GPC

description: RNA-seq, reanalysis of GSM2310229

value: schizophrenia


title: SCZ_164G GPC

description: RNA-seq, reanalysis of GSM2310227


title: H9-DE, Illumina, rep 1


title: Co2880-IT1

value: Cortex

value: 7 years

value: WT

tag: Sex


title: SCZ_164H GPC

description: RNA-seq, reanalysis of GSM2310228


title: JKB201_1_2_3

value: Peripheral blood


title: H1-PGC, Illumina, rep 3

value: H1-hESC derived primordial germ cell-like cells


title: H9-PE, Illumina, rep 3


title: H9-hESC, Illumina, rep 2


title: H1-PGC, Illumina, rep 1


title: H1-PE, Illumina, rep 3

value: H1-hESC derived pharyngeal endoderm


title: SCZ_164E GPC

description: RNA-seq, reanalysis of GSM2310225


title: H9-hESC, Illumina, rep 1


title: H1-PE, Illumina, rep 1


title: SCZ_164F GPC

description: RNA-seq, reanalysis of GSM2310226


title: JKB201_1_2_2


title: JKB201_1_1_3

value: day 3


title: H1-PE, Illumina, rep 2


title: JKB201_1_2_1


title: SCZ_164D GPC

description: RNA-seq, reanalysis of GSM2310223


title: H1-hESC, Illumina, rep 2

value: H1 human embryonic stem cells


title: H1-DE, Illumina, rep 1

value: H1-hESC derived definitive endoderm


title: H1-hESC, Illumina, rep 1


title: H1-DE, Illumina, rep 3


title: SCZ_164C GPC

description: RNA-seq, reanalysis of GSM2310222


title: JKB201_2_1_3_109046


title: HEK293T_dMut, Illumina, rep 3

value: human epithelial like cells


title: H1-DE, Illumina, rep 2


title: H1-hESC, Illumina, rep 3


title: SCZ_164B GPC

description: RNA-seq, reanalysis of GSM2310221


title: SCZ_164A GPC

description: RNA-seq, reanalysis of GSM2310219


title: JKB201_2_1_2_109045


title: HEK293T_WT, Illumina, rep 3


title: JKB201_1_1_1


title: CTR_37C GPC

description: RNA-seq, reanalysis of GSM2310216

value: control


title: CTR_37D GPC

description: RNA-seq, reanalysis of GSM2310217


title: HEK293T_dMut, Illumina, rep 2


title: HEK293T_dMut, Illumina, rep 1


title: HEK293T_WT, Illumina, rep 1


title: H1-PGC, Illumina, rep 2


title: CTR_37B GPC

description: RNA-seq, reanalysis of GSM2310215


title: JKB201_2_1_1_109044


title: JKB201_1_0_2


title: CTR_37A GPC

description: RNA-seq, reanalysis of GSM2310214


title: HEK293T_WT, Illumina, rep 2


title: JKB200_2_4_3_1_108323


title: hMSC, full-length spike, neutralizing antibody to S1, endothelin-1, rep3

city: Hung Hom, Kowloon

first: Lanlan

last: Zhang

address: 11 Yuk Choi Road

country: Hong Kong

institute: The Hong Kong Polytechnic University

description: Name in processed files: SAE-3

data_processing:
Preprocessing: Sequencing reads were first filtered for adapter sequence and low quality sequence followed by retaining only reads with read length ≥ 40bp. Low Quality is defined as: Reads with more than 5% unknown bases (“N”), or Reads having more than 50% of bases with quality value <= 11. Subsequently, sequencing reads were filtered for rRNA sequence and remaining reads were used for downstream analysis
Alignment: STAR Version 2.7.8
Quantify expression: RSEM Version 1.2.31
Identify differentially expressed genes: EBSeq Version 1.18.0
Assembly: Human Genome GRCh38
Supplementary files format and content: YuanSF_RNASeq_CPOS-230919-SY-19861a_Gene_DiffExpressed: DEGs of all comparisons
Supplementary files format and content: C_SP_clean: DEGs for comparison between Control and SP group
Supplementary files format and content: C_SAE_clean: DEGs for comparison between Control and SAE group
Supplementary files format and content: SP_SAE_clean: DEGs for comparison between SP and SAE group

source_name: human mesenchymal stem cells

extract_protocol:
As detailed in TRIzol Reagent User Guide  (Thermo Fisher, Pub.No. MAN0001271 C.0)
As detailed in KAPA mRNA HyperPrep Kit Technical Data Sheet (KR1352), with xGen Dual Index UMI Adapters

value: human mesenchymal stem cells


title: hMSC, full-length spike, neutralizing antibody to S1, endothelin-1, rep2

description: Name in processed files: SAE-2


title: hMSC, full-length spike, neutralizing antibody to S1, endothelin-1, rep1

description: Name in processed files: SAE-1


title: JKB200_2_4_2


title: CTR_22C GPC

description: RNA-seq, reanalysis of GSM2310213


title: hMSC, full-length spike, rep3

description: Name in processed files: SP-3


title: JKB200_2_4_1


title: hMSC, full-length spike, rep2

description: Name in processed files: SP-2


title: CTR_22B GPC

description: RNA-seq, reanalysis of GSM2310212


title: hMSC, full-length spike, rep1

description: Name in processed files: SP-1


title: JKB200_2_3_3


title: hMSC, Ctrl, rep3

description: Name in processed files: Ctrl-3


title: hMSC, Ctrl, rep2

description: Name in processed files: Ctrl-2


title: JKB200_2_3_2


title: hMSC, Ctrl, rep1

description: Name in processed files: Ctrl-1


title: CTR_22A GPC

description: RNA-seq, reanalysis of GSM2310211


title: JKB200_2_2_3_12_108329


title: IPSCs, patient, Hi-C

city: Guangzhou

first: Qingjiong

state: Guangdong

address: Sun Yat-sen University

country: China

institute: Zhongshan Ophthalmic Center

library_source: genomic

data_processing:
Hi-C data was processed using HiC-Pro pipline (v2.11.1).
Paired-end reads were aligned to the human reference genome (hg38) downloaded from the Ensembl genome browser
Mapped reads were filtered to retain only those with a mapping quality greater than 10 and paired by using ‘mergeSAM.py’ script in HiC-Pro pipeline.
Fragments involved in chromatin interactions from the mapped reads were extracted using 'mapped_2hic_fragments.py' script in HiC-Pro pipeline.
The contact maps were subjected to normalization using iterative correction and eigenvector decomposition (ICE) method and the normalized contact maps were converted to h5 format using ‘hicConvertFormat’ function of HiCExplorer (v3.5.1).
Assembly: hg38
Supplementary files format and content: Whole genome chromatin interaction frenquency file: AF.allValidPairs.hic
Supplementary files format and content: Whole genome chromatin interaction frenquency file: unAF.allValidPairs.hic

molecule: genomic DNA

extract_protocol:
Genomic DNA of cells was crosslinked in situ using serum-free DMEM with 2% formaldehyde and then were flash-frozen in liquid nitrogen before digested. The crosslinked cells were lysed and digested with MboI restriction enzyme. After biotinylated and ligated, the fragments were purified and assessed for quality. The qualified samples were reverse crosslinked and then submitted for library constructions.
Standard library constructions were performed, including sonication fragment, end repair, A-tailing, biotin enrichment, adapter ligation, and amplification.

value: IPSCs


title: IPSCs, control, Hi-C

value: normal


title: IPSCs, control, CUT&Tag, rep02

data_processing:
Cut&Tag data were aligned to the human reference genome (hg38) using 'bwa mem' of BWA (v0.7.15) with default parameters.
Reads with low mapping quality (MAPQ<20) reads were filtered out using ‘samtools view’ function of samtools (v1.3.1).
PCR duplicates were removed using ‘MarkDuplicates’ function of Picard.
H3K27ac modification peaks were identified using 'macs2 callpeak' function of MACS2 (v2.2.7.1) with default parameters.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

extract_protocol:
Cells was rinsed with PBS and dissociated with 0.5mM EDTA.
Resuspended cells were attached to Concanavalin A beads (Bangs Laboratories, IN, USA) and then were incubated with primary antibody against H3K27ac (Active motif, CA, USA). After washed, cells were incubated with pA-Tn5 (Vazyme, China). After quenching the fragmentation, the cells were added with proteinase K. Post-incubation, a phenol–chloroform–isoamyl alcohol mix wasused to extract DNA. The samples were incubated at -80°C freezer and subsequently centrifuged. The pellet was air dried and resuspended in a desired amount of EB buffer. DNA concentration was estimated using the Qubit. PCR amplification was performed using universal N5 primer and indexed N7 primer and PCR cycle number was optimized. Amplified products were purified using 1: 1.3X Ampure bead.

value: Normal

value: H3K27ac antibody (Active motif, #39133)


title: JKB200_2_2_2

value: BALB/c

value: day 2


title: IPSCs, control, CUT&Tag, rep01


title: CTR_205E GPC

description: RNA-seq, reanalysis of GSM2310208


title: IPSCs, patient, CUT&Tag, rep02


title: control_FOXO1_non-stimulated_stimulated2

city: Melbourne

first: Kevin

middle: C

last: sek

state: VIC

address: 305 Grattan Street

department: Cancer Immunology

institute: Peter MacCallum Cancer Centre

library_source: transcriptomic single cell

data_processing:
scRNA-seq data were generated using the 10x Cell Ranger pipeline (7.1.0) and hg38 genome. Specifically, cellranger multi was used to generate raw feature barcode matrices. Downstream analysis was performed in R (version 4.2.0). Empty droplets were detected and removed from the raw feature barcode matrix using the emptyDrops function from the DropletUtils (version 1.16.0) package and doublets were detected and removed using DoubletFinder (verison 2.0.3). Using Seurat (version 4.3.0), cells with less than 200 features and more than 5% mitochondrial reads were excluded. Standard Seurat data processing and normalization steps were performed: NormalizeData, FindVariableFeatures, ScaleData, RunPCA, RunUMAP, FindNeighbors and FindClusters; clusters with low-quality metrics were removed, and the final resolution was determined using results from the clustree package (version 0.5.0). LMOs were demultiplexed using HTODemux (Seurat). DEGs were calculated using the functions FindAllMarkers (Seurat) using a log2 fold change threshold of 0.125 and an adjusted P value of less than 0.05, and included the number of counts as a latent variable. Pseudobulk DEGs were detected using the Libra package (version 1.0.0) using the run_de function. Geneset enrichment was performed using the fgsea package with all expressed genes as the background gene list, which was ranked by average log fold change detected with FindMarkers using a log2 fold change threshold of 0 and min.pct parameter set to 0. To perform diffexp analyses and GSEA between individual groups within each cluster, the to_psuedobulk function from Libra was used to pull out pseudobulk count matrix of each replicate pool and clusters. EdgeR and fgsea was then utilized to perform differential expression and gsea analyses of reference gene signatures. The single-cell signature explorer program was utilized for visualization of gene signatures across UMAP plots.
Assembly: hg38 genome
Supplementary files format and content: Tab-separated values files and matrix files (output from Cellranger)

source_name: T cell

growth_protocol: Human peripheral blood mononuclear cells (PBMCs) were isolated from normal buffy coats using Ficoll centrifugation and PBMCs were cultured in RPMI supplemented with 10% FCS, sodium pyruvate, glutamax, NEAA, HEPES and penicillin/streptomycin. PBMCs were activated with antihuman CD3 (30ng/ ml) and IL-2 (600 IU/ml) for 48 hours before transduction with a lentvirus encoding a second generation scFv–anti–Lewis-Y CAR (41BBz and CD3ζ). Cells were cultured at a density of 1x106/ml following the transduction process.

extract_protocol:
Protocol for capture: Chromium Next GEM single cell 5’reagent kit v2
Protocol for gene expression and VDJ Library prep: Chromium Next GEM single cell 5’reagent kit v2 ( including Fragmentation, Ligation, Indexing)

treatment_protocol: Cultured without stimulation (non-stimulated), stimulated with MCF7 tumour cells for 24 h

value: T cell

tag: donor

value: Healthy donor

tag: genetic modification

value: α-Lewis-Y-CAR

value: control, FOXO1

value: no stimulation, stimulation with MCF7 tumour cells


title: JKB200_2_2_1

tag: strain

tag: tissue

value: Peripheral blood

value: day 1


title: CTR_205D GPC

description: RNA-seq, reanalysis of GSM2310207


title: IPSCs, patient, CUT&Tag, rep01

tag: cell type

tag: treatment


title: JKB200_2_1_2

tag: timepoint


title: control_FOXO1_non-stimulated_stimulated1


title: OVCAR-8-FOXM1-KD rep1

city: Chicago

first: Xu

state: Illinois

address: 820 South Wood St

institute: University of Illinois at Chicago

data_processing:
Sequencing data were aligned to human reference genome version GRCh38 annotated by Gencode version 43, using STAR version 2.5.1b.
Counts within genes were obtained by Feature Counts using subread version 1.5.0-p1.
Assembly: GRCh38
Supplementary files format and content: raw counts of gene expression in tab-delimited format

source_name: cell culture

growth_protocol: Cell lines were cultured in Dulbecco's Modified Eagle Medium (DMEM) with 4.5 g/L glucose and 4mM L-Glutamine (Gibco; Thermo Fisher Scientific). For all cell lines, the growth media was supplemented with 10% Foetal Bovine Serum (FBS), penicillin (100 U/mL), and 100 μg/mL streptomycin (Gibco; Thermo Fisher Scientific. All cell lines were grown and maintained at 37°C in a humidified incubator with 5% CO2. Sub-confluent cultures (70-80%) were split 1:5 using 0.25% Trypsin/EDTA (Millipore Sigma).

extract_protocol:
Total RNA from cultured cells was extracted and purified using TRIzol reagent (Fisher Scientific) and the PureLink™ RNA Mini Kit (Fisher Scientific) including on-column DNase (Thermo Fisher Scientific) treatment according to the manufacturer’s instructions. To assess the integrity of RNA, all samples were analyzed on the Agilent 4200 TapeStation (Agilent Technologies, USA). The remaining DNA concentrations were measured using the Qubit fluorometer (Thermo Fisher Scientific). In all the samples the DNA amounts did not exceed 2% of the total amount of nucleic acid.
Sequencing libraries for Illumina sequencing platform were created in one batch in a 96-well plate, we used Stranded CORALL Total RNA-Seq Library Prep kit (Lexogen, Austria) with Lexogen's RiboCop HMR rRNA Depletion Kit. In brief, in the first step during rRNA removal we used 260–660 ngs of total RNA, and then followed by library creation initiated with random oligonucleotide primer hybridization with complementary sequence within the RNA template and reverse transcription. No prior RNA fragmentation was done before reverse transcription, as the insert size was determined by proprietary size-restricting method. Next, Illumina-compatible P5 sequences and UMIs (Unique Molecular Identifiers) were ligated at the 3′ end of the first-strand cDNA fragments. During the following steps of the 2nd-strand cDNA synthesis and the double-stranded cDNA amplification, unique i5 and i7 index sequences as well as complete adapter sequences required for cluster generation were added. The number of PCR amplification cycles was 12, as determined by qPCR using a small pre-amplification library aliquot for each sample.

treatment_protocol: After harvesting, cells were counted in presence of Trypan Blue (Thermo Fisher Scientific) and seeded onto tissue culture plates to achieve ~50% confluency. The next day, treatment of cells was performed by aspirating the nonadherent cells and growth medium and replacing it with the fresh one containing selected concentrations of drugs. For Tamoxifen based studies, the nonadherent cells and growth media was aspirated and replaced with the DMEM supplemented with 4.5 g/L glucose and 4mM L-Glutamine, 10% FBS, penicillin (100 U/mL), 100 μg/mL streptomycin, 10nM estrogen, and selected concentrations of drugs. The vehicle control groups were treated using the solvent of the drug, vehicle concentration did not exceed 0.3%. Post-treatment at selected times, the cells were harvested, washed with ice-cold PBS.

value: cell culture

value: cancer cell line


title: CTR_205B GPC

description: RNA-seq, reanalysis of GSM2310205

value: control


title: CTR_205C GPC

description: RNA-seq, reanalysis of GSM2310206


title: OVCAR-8-STL001 rep2


title: JKB200_2_1_1


title: OVCAR-8-STL001 rep1


title: CTR_205A GPC

description: RNA-seq, reanalysis of GSM2310204


title: JKB200_2_0_3

value: day 3


title: CTR_205G GPC

description: RNA-seq, reanalysis of GSM2310210


title: CTR_205F GPC

description: RNA-seq, reanalysis of GSM2310209


title: OVCAR-8-Control rep2


title: OVCAR-8-Control rep1


title: FLO1-STL001 rep2


title: FLO1-Control rep2


title: FLO1-STL001 rep1


title: HD20D Astrocyte

description: RNA-seq, reanalysis of GSM3394752

source_name: Astrocyte induced from ESC

value: Huntington's disease


title: JKB200_2_0_2


title: JKB200_2_1_3


title: FLO1-Control rep1


title: HD20B Astrocyte

description: RNA-seq, reanalysis of GSM3394750


title: JKB200_2_0_1


title: CD19, invitro, Donor 3

city: Bronx

first: Christopher

last: Nishimura

address: 1300 Morris Park Avenue

institute: Albert Einstein College of Medicine

data_processing:
Paired-end reads from RNA sequencing were aligned using the STAR aligner (version 2.6.1b) to the human reference genome (hg38).
Gene-mapped fragments were counted using HTseq software (version 0.6.1), with an average expression count of 1 or more used as a threshold for expression determination.
Assembly: hg38
Supplementary files format and content: tab-delimited text file of count matrix

source_name: CAR-transduced human T cells

growth_protocol: T cells were activated using OKT3/CD28 antibodies and then transduced using CAR lentivirus. CAR-T cells were cultured in CTS OpTmizer media supplemented with IL7/15.

extract_protocol:
RNA was extracted using the Qiagen RNeasy plus mini kit according to the manufacturer's directions.
Libraries were constructed by Admera Health using NEBNext Ultra II.

treatment_protocol: CAR-T cells were cocultured with HCC827 tumor cells for 24 hours.

value: CAR-transduced human T cells

value: Coculture CD19


title: OVCAR-8-FOXM1-KD rep2


title: CD19, invitro, Donor 2


title: HD18B Astrocyte

description: RNA-seq, reanalysis of GSM3394747


title: HD20A Astrocyte

description: RNA-seq, reanalysis of GSM3394749


title: HD18A Astrocyte

description: RNA-seq, reanalysis of GSM3394746


title: B7H3_CD28_41BB, invitro, Donor 4

value: Coculture CD28.4-1BB


title: CD19, invitro, Donor 4


title: JKB200_1_4_1_5_108330

value: BALB/c


title: B7H3_CD28_41BB, invitro, Donor 3


title: B7H3_CD28_41BB, invitro, Donor 2


title: JKB200_1_4_2

value: day 2


title: CD19, invitro, Donor 1


title: JKB200_1_3_2_11_108313


title: HD17E Astrocyte

description: RNA-seq, reanalysis of GSM3394745


title: HD17D Astrocyte

description: RNA-seq, reanalysis of GSM3394744


title: B7H3_TMIGD2, invitro, Donor 4

value: Coculture TMIGD2


title: B7H3_TMIGD2, invitro, Donor 3


title: HD17C Astrocyte

description: RNA-seq, reanalysis of GSM3394743


title: B7H3_TMIGD2, invitro, Donor 2


title: B7H3_TMIGD2, invitro, Donor 1


title: CD28_41BB, invivo, Donor 5

data_processing:
Paired-end reads from RNA sequencing were aligned using the STAR aligner (version 2.7.9a) to the human reference genome (hg38).
The alignment data were then used by the RSEM software (version 1.3.3) to quantify expression levels of individual genes (both coding and non-coding) in the GENCODE annotation (version 41), yielding estimated read counts and transcripts per million (TPMs).
Genes with a TPM < 1 in all samples were excluded from further analysis
Assembly: hg38
Supplementary files format and content: xls file includes gene names, TPM and raw counts

source_name: From lung tissue-infiltrating T cells

extract_protocol:
RNA was extracted using the Qiagen RNeasy plus mini kit according to the manufacturer's directions.
Libraries were constructed by Admera Health using SMARTseq V4.

treatment_protocol: CAR-T cells were intravenously injected into mice bearing HCC827 lung tumors.

value: From lung tissue-infiltrating T cells

value: Intravenous injection CAR-T cells


title: JKB200_1_2_3_7_108317


title: CD28_41BB, invivo, Donor 4


title: JKB200_1_2_2_10_108316


title: HD17B Astrocyte

description: RNA-seq, reanalysis of GSM3394742


title: JKB200_1_4_3


title: CD28_41BB, invivo, Donor 3


title: CD28_41BB, invivo, Donor 2


title: JKB200_1_2_1_3_108315


title: TMIGD2, invivo, Donor 5


title: CTR19D Astrocyte

description: RNA-seq, reanalysis of GSM3394740


title: B7H3_CD28_41BB, invitro, Donor 1


title: TMIGD2, invivo, Donor 4


title: JKB200_1_1_3_6_108320


title: TMIGD2, invivo, Donor 3


title: JKB200_1_1_2_9_108319


title: JKB200_1_3_1_4_108312


title: TMIGD2, invivo, Donor 2


title: CTR19B Astrocyte

description: RNA-seq, reanalysis of GSM3394738


title: CTR19A Astrocyte

description: RNA-seq, reanalysis of GSM3394737


title: JKB200_1_1_1_2_108318


title: HD17A Astrocyte

description: RNA-seq, reanalysis of GSM3394741


title: CD28_41BB, invitro, Donor 3

data_processing:
Paired-end reads from RNA sequencing were aligned using the STAR aligner (version 2.7.9a) to the human reference genome (hg38).
The alignment data were then used by the RSEM software (version 1.3.3) to quantify expression levels of individual genes (both coding and non-coding) in the GENCODE annotation (version 41), yielding estimated read counts and transcripts per million (TPMs).
Genes with a TPM < 1 in all samples were excluded from further analysis
Assembly: hg38
Supplementary files format and content: xls file includes gene names, counts, raw counts, and TPMs.

treatment_protocol: CAR-T cells were cocultured with HCC827 tumor cells for 72 hours.

value: Coculture CD28_41BB


title: CTR02C Astrocyte

description: RNA-seq, reanalysis of GSM3394735


title: JK203_2_3_2_109054


title: TMIGD2, invitro, Donor 4


title: TMIGD2, invitro, Donor 3


title: HD20G GPC

description: RNA-seq, reanalysis of GSM2816802

source_name: GPC induced from ESC


title: JK203_2_3_1_109053


title: HD20F GPC

description: RNA-seq, reanalysis of GSM2816801


title: TMIGD2, invitro, Donor 2


title: JK203_2_2_3_109052


title: H1944 BAY1217389 bio rep 2

city: Tokyo

first: Shunsuke

last: Kitajima

department: Department of Cell Biology

country: Japan

institute: Japanese Foundation for Cancer Research

data_processing:
Macrogen Incorporated
Assembly: hg18
Supplementary files format and content: tab-delimited text files include RPKMvalues for each sample

source_name: Lung

growth_protocol: H1944 cells were cultured in RPMI 1640 (supplemented with 10% FBS, and 1x penicillin-streptomycin.

extract_protocol:
RNA extraction was performed using RNeasy Mini Kit (Qiagen, Cat.# 74106). Total RNA concentration was calculated by Quant-IT RiboGreen (Invitrogen, #R11490).
RNA library was prepared by Illumina TruSeq Stranded mRNA Sample Prep Kit following the manufacture’s protocol.

treatment_protocol: Cells were treated with DMSO or the MPS1i BAY1217389 for 48 h, followed by 24 h washout and RNA sequencing

value: Lung

value: lung cancer cell line


title: H1944 BAY1217389 bio rep 1


title: CTR19C Astrocyte

description: RNA-seq, reanalysis of GSM3394739


title: H1944 DMSO bio rep 2

value: DMSO


title: JK203_2_2_2_109051

value: Peripheral blood


title: CD28_41BB, invitro, Donor 4


title: CD28_41BB, invitro, Donor 5


title: JK203_2_2_1_109050

value: day 1


title: HD20D GPC

description: RNA-seq, reanalysis of GSM2816799


title: Pt-19 [ATAC-seq]

first: Franco

last: Izzo

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

description: Fragment file obtained after processing of raw scATAC sequencing files through the cell-ranger-atac (v2.0.0) pipeline and amplicons obtained from the GoT-ChA library

library_source: genomic single cell

data_processing:
FASTQ files were processed through the cell-ranger-atac (v2.0.0). Single cell ATAC-seq metadata files were generated by analysis with ArchR (v1.0.0),  Gotcha (v1.0.0) and GotchaMito (v1.0.0)
Assembly: hg38
Supplementary files format and content: Fragment files output from cell-ranger-atac (v2.0.0) pipeline as tab separated files. Metadata including cell cluster and genotype assignments is available as .csv files.

source_name: Peripheral blood mononuclear cells (PBMC)

growth_protocol: Human CA46 (ATCC, #CRL-1648), HEL (ATCC, #TIB-180), SET-2 (DSMZ, #ACC 608) and CCRF-CEM (ATCC, #CRM-CCL-119) cell lines were maintained according to standard procedures in RPMI-1640 (Thermo Fisher Scientific, #11-875-119) with 10% (or 20% for CA46 and SET-2 cells) FBS (Thermo Fisher Scientific, #10-437-028) at 37˚C with 5% CO2. Cell lines in culture were screened biweekly for mycoplasma contamination using the MycoAlert PLUS Mycoplasma Detection Kit (Lonza, #LT07-703).

extract_protocol:
Patient samples were FACS-sorted using CD34+ DAPI- gating. Downstream processing using the 10X Chromium Solution platform for single cell ATAC sequencing, with the modifications of the GoT-ChA protocol.
Nuclei were subsequently processed according to the Chromium Next GEM Single Cell ATAC Solution user guide (version CG000209 Rev F, 10x Genomics) with the following modifications: 1- During the GEM Generation and Barcoding reaction (Step 2.1), 1 μL of 22.5 μM GoT-ChA primer mix was added to the barcoding reaction mixture. The primers used are GoT-ChA_R1N (locus-specific primer with a Read 1N handle sequence: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG - [22bp locus specific]) and GoT-ChA_IS2 (locus- specific primer with an IS2 handle sequence: AGCAAGTGAGAAGCATCGTGTC - [22bp locus specific]). These primers allow for exponential amplification of the GoT-ChA fragments, relative to the linear amplification of ATAC fragments. 2- During the Post GEM Incubation Cleanup (Step 3.2), 45.5 μL of Elution Solution I is used to elute material from SPRIselect beads. 5 μL is used for GoT-ChA library construction, and the remaining 40 μL are used for ATAC library construction as indicated in the standard protocol. 3 - To generate the GoT-ChA library, two additional PCRs were performed on the 5 μL set aside during Step 3.2. The first PCR aims to amplify genotyping fragments prior to sample indexing and uses P5 (binds the P5 Illumina sequencing handle: AATGATACGGCGACCACCGAGATCTACAC) and GoT- ChA_nested (a nested, biotinylated, locus specific primer with a TruSeq Small RNA Read 2 handle: /5BiosG/CCTTGGCACCCGAGAATTCCA-[22bp locus specific]) primers with the following thermocycler program: 95 °C for 3 min; 15 cycles of 95 °C for 20 s, 65°C for 30 s and 72°C for 20 s; followed by 72°C for 5 min and ending with hold at 4°C. After a 1.2X SPRIselect clean up, biotinylated PCR product is bound and isolated using Dynabeads M-280 Streptavidin magnetic beads (Thermo Fisher Scientific, #11206D). Briefly, beads are washed three times with 1X sodium chloride-sodium phosphate-EDTA buffer (SSPE, VWR, #VWRV0810- 4L), added to the purified PCR product, and incubated at room temperature for 15 minutes. The beads are then washed twice with 1X SSPE buffer and once with 10 mM Tris-HCl (pH 8.0) before resuspending in water. The bead-bound fragments are then amplified and sample indexed using P5 and RPI-X (binds the TruSeq Small RNA Read 2 handle and adds a sample index and P7 Illumina sequencing handle: CAAGCAGAAGACGGCATACGAGATXXXXXXXXGTGAC TGGAGTTCCTTGGCACCCGAGAATTCCA, “X” denotes user-defined sample index) primers with the following thermocycler program: 95 °C for 3 min; 6- 10 cycles of 95 °C for 20 s, 65°C for 30 s and 72°C for 20 s; followed by 72°C for 5 min and ending with hold at 4°C
ATAC libraries were sequenced to a depth of 25,000 read pairs per nucleus and GoT-ChA libraries were sequenced to 5,000 read pairs per nucleus

tag: mpn subtype

value: Clonal Hematopoiesis

value: Untreated


title: JK203_2_3_3_109055

value: day 3


title: HD20C GPC

description: RNA-seq, reanalysis of GSM2816798

value: Huntington's disease


title: CD28_41BB, invitro, Donor 2

description: Downsampled due to library overload

value: CAR-transduced human T cells


title: TMIGD2, invitro, Donor 5


title: JK203_2_1_3_109049


title: Pt-17 [ATAC-seq]

value: Myelofibrosis


title: Pt-18 [ATAC-seq]

value: Ruxolitinib


title: HD20A GPC

description: RNA-seq, reanalysis of GSM2816797


title: Pt-16 [ATAC-seq]


title: JK203_2_1_2_109048

value: BALB/c

value: day 2


title: HD18F GPC

description: RNA-seq, reanalysis of GSM2816796


title: HD20E GPC

description: RNA-seq, reanalysis of GSM2816800


title: Pt-13 [ATAC-seq]


title: JK203_2_1_1_109047


title: H1944 DMSO bio rep 1


title: Pt-12


title: JKB201_2_2_3_6_108359


title: HD18D GPC

description: RNA-seq, reanalysis of GSM2816795


title: HD18C GPC

description: RNA-seq, reanalysis of GSM2816794


title: Pt-2 - Processed with DOGMA-seq protocol

description: Fragment files, RNA and protein (CITE-seq) count matrices obtained after processing of raw DOGMA-sequencing files through the cell-ranger-arc (v2.0.2) pipeline


title: Pt-11 [ATAC-seq]


title: Pt-10 [ATAC-seq]


title: Pt-09 [ATAC-seq]


title: Pt-08 [ATAC-seq]


title: HD18B GPC

description: RNA-seq, reanalysis of GSM2816793


title: JKB201_2_2_2_4_108358


title: Multiplexing_adapted

description:
Cell line mixture experiment to determine multiplexing capacity in adapted setting
Cell mixing experiment containing HEL, SET-2, CA46 and OCI-AML3 cell lines targeting JAK2-V617F, TP53-M133, NRAS-Q61and TP53-R248 using adapted GoT-ChA protocol for multiplexing

source_name: Cell line mixture 1:1:1:1 (HEL, SET-2, CA46 and OCI-AML3)


title: JKB201_2_0_1_12_108354


title: Multiplexing_original_protocol

description:
Cell line mixture experiment to determine multiplexing capacity
Cell mixing experiment containing HEL, SET-2, CA46 and OCI-AML3 cell lines targeting JAK2-V617F, TP53-M133, NRAS-Q61and TP53-R248


title: HD18A GPC

description: RNA-seq, reanalysis of GSM2816792


title: HD17F GPC

description: RNA-seq, reanalysis of GSM2816791


title: Pt-15 [ATAC-seq]


title: K562, Y391K-LSD1-GFP, edited2-2

city: Boston

first: Kwangwoon

last: Lee

state: MA

address: 77 Avenue Louis Pasteur, NRB 164

department: Medicine

institute: Brigham and Women's Hospital

data_processing:
Initial data quality assessment was performed using FastQC (v0.11.8). Adapter trimming was accomplished using fastq-mcf (v1.05) and cutadapt (v2.5). Bowtie2 (v2.5.1) was employed to eliminate unwanted sequences, including mitochondrial genome sequences, ribosomal RNAs, and adapter sequences. The paired-end reads were then aligned to the reference human genome Feb. 2009 release (GRCh37/hg19) obtained from the UCSC database. The chromosome fasta file was sourced from (http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz), and the GTF file from (ftp://ftp.ensembl.org/pub/release75/gtf/homo_sapiens/Homo_sapiens.GRCh37.75.gtf.gz). Alignment was executed using STAR (v2.7.3a). Aligned reads were utilized to estimate gene expression levels. Raw read counts were determined using HTSeq (v0.11.2) and normalized using DESeq2. The cufflinks software (v2.2.1) was employed to estimate gene expression in Fragments per kilobase per million (FPKM) units. Rigorous quality control was conducted using RNA-SeQC (v1.1.8), RSeQC (v3.0.1), and MultiQC (v1.7).
DESeq2 (R Bioconductor package) facilitated differential expression analysis. Specifically, it compared the combinations of parental cells (control) and edited cells, assessing the number of significantly differentially expressed protein-coding genes without fold change shrinkage. The results of up and downregulated genes in the edited K562 cells were visualized through a volcano plot with the significance (-log10 p value) and log2 fold changes, relative to the parental K562 cells.
Assembly: hg19
Supplementary files format and content: excel file containing raw counts and normalized counts for each sample
Supplementary files format and content: excel file containing FPKM values for each sample
Supplementary files format and content: excel file containing differential gene expression analysis (DESeq2) with shrinkage
Supplementary files format and content: excel file containing differential gene expression analysis (DESeq2) without shrinkage

growth_protocol: RPMI1640, 10% fetal bovine serum, 2 mM L-glutamine, 1x penicillin/streptomycin. Cells were cultured at 37 degrees C and 8% CO2

extract_protocol:
The harvested cell pellets were flash-frozen and sent to MedGenome (Foster City, CA) for RNA extraction, sequencing, and analysis. Extractions were carried out using a Maxwell RSC simplyRNA Cells Kit (Promega, cat 1390).  To verify RNA quality, RNA qualitative and quantitative assessment was done using Qubit 3.0 (life technology, cat Q33216) and TapeStation 4200 (Agilent) confirming that the RNA Integrity Number equivalent (RINe) score exceeded 8.9 for all samples.
The Poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads and then mRNA was converted to cDNA, library preparation using TruSeq Stranded mRNA Library Prep Kit (cat 20020595) according to the manufacturer’s protocol. Libraries were sequenced for PE150 cycles to a depth of 40 million paired reads using Illumina NovaSeq 6000.

treatment_protocol: Parental K562 cells are homozygously edited with LSD1-GFP. Edited K562 cells are heterozygously edited with Y391K-LSD1-GFP (2 alleles with Y391K-LSD1-GFP and 1 allele with wt-LSD1-GFP)

value: human immportalized chronic myelogenous leukemia


title: K562, Y391K-LSD1-GFP, edited2-1


title: JKB201_1_3_3_11_108353


title: K562, Y391K-LSD1-GFP, edited1-1


title: K562, Y391K-LSD1-GFP, edited1-2


title: Pt-14 [ATAC-seq]


title: JKB201_1_3_1_10_108351


title: HD17E GPC

description: RNA-seq, reanalysis of GSM2816790


title: K562, wtLSD1-GFP, parental3


title: HD17C GPC

description: RNA-seq, reanalysis of GSM2816789


title: K562, wtLSD1-GFP, parental1


title: JKB201_1_1_2_8_108346


title: JKB201_1_0_3_3_108350


title: THP1 GR H3K27me3 rep1

city: Singapore

first: KAIJING

last: CHEN

address: 60 Nanyang Drive

department: school of biological science

country: Singapore

institute: Nanyang Technological University

data_processing:
The paired-end reads were aligned with bowtie2 (v 2.3.5.1) using the following flag parameters: --local, --very-sensitive-local, --no-unal, --no-mixed, --no-discordant, --phred33, -I 10, and -X 700.
The resulting SAM files were then converted to BAM files and sorted with the samtools (v 1.10) and Picard (https://github.com/broadinstitute/picard, v 2.27.5-4) software.
After removing reads mapped to chrM, chrUn, and ‘random’ chromosome, BAM files of replicates were sorted and combined using the samtools (v 1.10) sort and merge function.
Merged BAM files were converted to BigWig files with RPKM normalization using deeptools bamCoverage (v 3.4.3) for data visualization on UCSC Genome Browser.
Peaks were called using MACS2 (v 2.2.7.1) with parameters "--nomodel --extsize mean fragment size of the sequencing library", and only peaks not contained in the ENCODE (v2) hg19 blacklist were retained.
genome build/assembly: hg19
Supplementary files format and content: broadPeak files include cut and run peaks called by MACS2
Supplementary files format and content: bigWig

growth_protocol: CRISPR knockout cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum, and 1% penicillin-streptomycin. K562 and THP1 cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum, and 1% penicillin-streptomycin.

extract_protocol:
All the Cut & Run experiments were performed using CUTANA Cut & Run prep Kit (14-1048, EpiCypher) according to the manufacturer's instructions. Cells were subsequently permeabilized with 0.01% digitonin and incubated with CTCF antibodies (EPR18253, Abcam) or H3K27me3 antibodies (C36B11, Cell signaling Technology) at 4℃ overnight. 0.5 ng of E. coli Spike-in DNA was added to each sample for normalization.  The K-MetStat Panel was spiked into H3K27me3 Cut & Run sample as an internal control.
Library construction was performed using the CUTANA Cut & Run Library Prep Kit (14-1002, EpiCypher) according to the manufacturer's instructions. All libraries were amplified using 14 cycles on the thermocycler. The DNA fragments with target sizes ranging from 200 bp to 1000 bp were selected using AMPure XP beads (Beckman Coulter) and validated using the Agilent High Sensitivity DNA kit.
OTHER: Cut & Run

treatment_protocol: EV, S1KO, S2KO and DKO K562 cells were generated using the all-in-one CRISPR/Cas9 vector system. K562 and THP1 cells were either treated with 0.1% DMSO or combined treatment of GSK343 (5 uM) and X5050 (100 uM) for 24 hr.

tag: cut and_run_antibody

value: treated with GSK343 and X5050 for 72 hours


title: JKB201_2_2_1_1_108357

data_processing:
Agilent TapeStation for quality control of DNA integrity.
Paired-end (2 × 300 bp) high-throughput sequencing was performed using the Illumina MiSeq platform.
Data processing, aggregation of UMIs and alignment of CDR3 sequences to the IMGT/V-QUEST reference genome were performed using repertoire analysis software based on MIGEC and MiXCR pipelines. Only sequences with UMIs were aligned.
TCRβ clones (defined by the CDR3 amino acid sequence) were excluded if they were less than 8 or greater than 20 amino acids in length, included a stop codon or a frameshift.
Assembly: IMGT/V-QUEST reference genome
Supplementary files format and content: txt files
Supplementary files format and content: clonotype tables
Library strategy: TCR-seq


title: THP1 GR H3K27me3 rep2


title: THP1 Ctrl H3K27me3 rep2

value: treated with 0.1% DMSO


title: CTR19H GPC

description: RNA-seq, reanalysis of GSM2816786

data_processing:
The sequencing reads were pre-processed with fastq(Chen et al., 2018), aligned with STAR (Dobin et al., 2013) to the genome assembly GRCh38 (Flicek et al., 2014), and quantified with RSEM (Li and Dewey, 2011) using the ENSEMBL Homo sapiens version 95 annotation.
Genome_build: GRCh38
Supplementary_files_format_and_content: RawCounts
Supplementary_files_format_and_content: TPM

value: control


title: JKB201_1_0_1_2_108348


title: THP1 Ctrl H3K27me3 rep1


title: K562 GR H3K27me3 rep2


title: JKB201_2_0_2_3_108355


title: K562 Ctrl H3K27me3 rep1


title: K562 Ctrl H3K27me3 rep2


title: K562 GR H3K27me3 rep1


title: S2 CTCF rep2

data_processing:
The paired-end reads were aligned with bowtie2 (v 2.3.5.1) using the following flag parameters: --local, --very-sensitive-local, --no-unal, --no-mixed, --no-discordant, --phred33, -I 10, and -X 700.
The resulting SAM files were then converted to BAM files and sorted with the samtools (v 1.10) and Picard (https://github.com/broadinstitute/picard, v 2.27.5-4) software.
After removing reads mapped to chrM, chrUn, and ‘random’ chromosome, BAM files of replicates were sorted and combined using the samtools (v 1.10) sort and merge function.
Merged BAM files were converted to BigWig files with RPKM normalization using deeptools bamCoverage (v 3.4.3) for data visualization on UCSC Genome Browser.
Peaks were called using MACS2 (v 2.2.7.1) with parameters "--nomodel --extsize mean fragment size of the sequencing library", and only peaks not contained in the ENCODE (v2) hg19 blacklist were retained.
genome build/assembly: hg19
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

value: CTCF

value: knockout silencer2 region


title: JKB201_1_3_2_2_108352

value: Peripheral blood


title: S2 CTCF rep1


title: FGF18 CTCF rep1

value: knockout silencer1 region


title: K562, wtLSD1-GFP, parental2


title: FGF18 CTCF rep2


title: CTR19D GPC

description: RNA-seq, reanalysis of GSM2816784


title: JKB200_1_3_3_108314


title: CTR19B GPC

description: RNA-seq, reanalysis of GSM2816782


title: EV CTCF rep1

value: untreated


title: JK4_1_2_2_RT_8

source_name: Tumour

value: Tumour

value: day 13


title: CTR19C GPC

description: RNA-seq, reanalysis of GSM2816783


title: HD17A GPC

description: RNA-seq, reanalysis of GSM2816787

value: Huntington's disease


title: HD17B GPC

description: RNA-seq, reanalysis of GSM2816788


title: EV CTCF rep2


title: DKO CTCF rep2

value: knockout silencer1 and 2 regions


title: JK4_1_2_2_RT_4


title: CTR19A GPC

description: RNA-seq, reanalysis of GSM2816781


title: JKB200_2_3_1_9_108342

value: day 1


title: CTR02F GPC

description: RNA-seq, reanalysis of GSM2816780


title: GR 72h rep2

data_processing:
Adaptors were trimmed by TrimGalore (0.6.6) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
Trimmed sequence reads were mapped to hg19 in pair-end mode using bowtie2 (v2.3.5.1) with default parameters.
The resulting SAM files were converted to BAM format and filtered to exclude reads with a mapq score below 30 using samtools (v1.10).
The BAM files were sorted, and duplicate reads were removed using through Picard (https://github.com/broadinstitute/picard, v 2.27.5-4).
After removing reads mapped to chrM, chrUn, and 'random' chromosomes, BAM files from replicates were merged.
Then merged bam files were converted to BigWig files with RPKM normalization using deeptools bamCoverage (v3.4.3) for data visualization on the UCSC Genome Browser.
Peaks were called using MACS2 (v2.2.7.1) (PMID: 24743991) callpeak with the following flag parameters: --shift -100 --extsize 200 --nomodel -B --SPMR -g hs, and peaks contained in the ENCODE (v2) hg19 blacklist were removed.
Assembly: hg19
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak files were generated using MACS v2 with default settings.

growth_protocol: CRISPR knockout and K562 wild-type cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum, and 1% penicillin-streptomycin. All cultures were maintained at 37 °C, 5% CO2 in a humidified incubator.

extract_protocol:
ATAC-seq was performed using the Diagenode ATAC-seq Kit (C01080002, Diagenode) following the manufacturer’s protocol. Briefly, 200,000 EV, S1KO, S2KO and DKO K562 cells or 50,000 drug-treated cells per sample were harvested and nuclei were isolated. Immediately following the nuclei prep, the pellet was resuspended in 50 µl tagmentation mix. The transposition reaction was carried out for 30 min at 37C. The tagmented DNA was then purified and eluted in 12 µl of DNA Elution Buffer.
Library was constructed using 10 µl of tagmented DNA and 1 µl of primer pair provided by the 24 UDI for Tagmented libraries Set I (C01011034, Diagenode)  following the manufacturer’s protocol. Libraries were amplified using 11-16 cycles on the thermocycler. The DNA fragments with target sizes ranging from 200 bp to 1000 bp were selected using AMPure XP beads (Beckman Coulter) and validated using the Agilent High Sensitivity DNA kit.

treatment_protocol: EV, S1KO, S2KO and DKO K562 cells were generated using the all-in-one CRISPR/Cas9 vector system. K562 wild-type cells were either treated with 0.1% DMSO or combined treatment of GSK343 (5 uM) and X5050 (100 uM) for 72 hr.


title: CTR19F GPC

description: RNA-seq, reanalysis of GSM2816785


title: DKO CTCF rep1


title: JK4_1_2_2_LT_8

extract_protocol:
Sorted cells were stored at -80C. RNA was extracted from frozen cells using the RNeasy Plus Micro Kit.
TCRβ amplicon libraries were generated with 5’Rapid Amplification of cDNA Ends (5’RACE) technology. RNA was transcribed to cDNA with a TCRβ constant region primer and a modified SMARTerIIA primer (Integrated DNA Technologies), with 9nt long unique molecular identifiers (UMI) added to individual TCRβ cDNA sequences. TCRβ locus was amplified by nested PCR with an additional TCRβ constant region primers, and a universal primer to SMARTerIIA, with the final PCR adding sequencing adaptors and barcodes to the TCRβ libraries. Products after each PCR were purified using AMPure XP AgenCourt Beads (Beckman Coulter).


title: GR 72h rep1


title: CTR02E GPC

description: RNA-seq, reanalysis of GSM2816779

extract_protocol: Glial cell populations where used in mRNA isolation by PolyA selection and mRNA sequencing analysis, utilizing the TruSeqRNA Library Prep Kit V2.


title: JK4_1_2_2_LT_4


title: DMSO 72h rep1


title: JK4_1_2_1_RT_8


title: CTR02D GPC

description: RNA-seq, reanalysis of GSM2816778


title: Thimme_08_rHBV.CD4_PD1positive

city: Basel

first: Jitao David

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

country: Switzerland

institute: F. Hoffmann-La Roche

description:
Thimme_08_S4
Peripheral blood mononucleated cell
P18_3.2_new_CD4_PD1hi

data_processing:
Reads were mapped to mouse genome GRCm38/mm10 with STAR.
Count data was generated with the bksnake pipeline.
Assembly: GRCm38/mm10
Supplementary files format and content: ThimmeHBVTcell_counts_merged_20230528.gct contains gene counts of all samples.

source_name: CD4 PD1+ T cells

extract_protocol:
Cells were isolated and FACS sorted based on CD4, CD8, and PD-1 expression.
CD8 T cells were directly sorted into 96 well plates prepared with 1X Reaction Buffer consisting of lysis buffer and RNase Inhibitor for low input RNA sequencing (Takara Bio, USA). Plates were spun down and immediately stored on dry ice or at -80°C until further processing. Sample plates containing lysed T cells were subjected to cDNA library preparation using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio, USA) followed by sequencing library preparation using the Nextera XT DNA Library Preparation Kit (Illumina) as per manufacturer’s instructions with minor modifications. Briefly, full-length cDNA was generated by reverse-transcription, template-switching reaction and PCR pre-amplification of polyadenylated mRNA as previously described. cDNA libraries were quantified using the Qubit dsDNA High Sensitivity Kit and quality was assessed on a Bioanalyzer using DNA High Sensitivity chips (Agilent). Double-stranded cDNA was subjected to fragmentation and PCR-based addition of Illumina barcoded sequencing adapters at both fragment ends. Sequencing library quantity and quality was assessed as described above.

value: CD4 PD1+ T cells

tag: cell number

tag: sample id

tag: patient id

tag: experiment day (facs run)

tag: sample number on experiment day

tag: bleed date

tag: diagnosis

value: rHBV

value: <10 IU/mL

tag: hbv dna [iu/ml]

tag: hbsag [iu/ml]

tag: hbeag [pei u/ml]

tag: hbv genotype


title: Thimme_07_HV.CD4_PD1positive

description:
Thimme_07_S3
Peripheral blood mononucleated cell
P01_1.2_new_CD4_PD1hi

tag: age

value: HV


title: Thimme_02_rHBV.CD4_PD1negative

description:
Thimme_02_S2
Peripheral blood mononucleated cell
P20_3.3_new_CD4_PD1low

source_name: CD4 PD1- T cells

tag: cell type

value: CD4 PD1- T cells


title: JK4_1_2_1_RT_4

tag: strain

value: BALB/c

tag: tissue


title: CTR02C GPC

description: RNA-seq, reanalysis of GSM2816777

tag: disease

value: control


title: P11_CD4_PD1hi

description:
90_S67
Peripheral blood mononucleated cell

value: cHBV

tag: treatment

value: A


title: Thimme_01_HV.CD4_PD1negative

description:
Thimme_01_S1
Peripheral blood mononucleated cell
P05_1.3_new_CD4_PD1low

tag: cell number


title: CTR02B GPC

description: RNA-seq, reanalysis of GSM2816776


title: JK4_1_2_1_LT_8

tag: timepoint


title: DMSO 72h rep2

tag: cell line

value: treated with 0.1% DMSO


title: P05_CD4_PD1hi

description:
89_S66
Peripheral blood mononucleated cell

tag: sample id

tag: patient id

tag: experiment day (facs run)


title: P12_CD4_PD1low

description:
87_S65
Peripheral blood mononucleated cell

tag: sample number on experiment day

tag: bleed date

tag: diagnosis

value: D


title: CTR02A GPC

description: RNA-seq, reanalysis of GSM2816775


title: JK4_1_2_1_LT_4


title: SCZ_8C Astrocyte

description: RNA-seq

source_name: Astrocyte induced from iPSC

value: schizophrenia


title: P23_CD4_PD1low

description:
84_S63
Peripheral blood mononucleated cell

tag: hbv dna [iu/ml]

tag: hbsag [iu/ml]

tag: hbeag [pei u/ml]


title: P22_Bulk_CD8

description:
83_S62
Peripheral blood mononucleated cell

source_name: Bulk CD8 T cells

tag: cell type

value: Bulk CD8 T cells

tag: age

tag: hbv genotype


title: P21_CD4_PD1low

description:
85_S64
Peripheral blood mononucleated cell


title: SCZ_8B Astrocyte

description: RNA-seq

tag: disease


title: P07_Bulk_CD8

description:
82_S61
Peripheral blood mononucleated cell

tag: treatment

value: Viread


title: JK4_1_2_0_RT_4

tag: strain

tag: tissue

value: Tumour

value: day 13


title: JK4_1_2_0_RT_8

tag: timepoint


title: SCZ_8A Astrocyte

description: RNA-seq


title: P15_CD4_PD1low

description:
79_S59
Peripheral blood mononucleated cell

tag: cell number

tag: sample id


title: P14_CD4_PD1hi

description:
80_S60
Peripheral blood mononucleated cell

tag: patient id

tag: experiment day (facs run)


title: P22_CD4_PD1low

description:
78_S58
Peripheral blood mononucleated cell

tag: sample number on experiment day

tag: bleed date


title: SCZ_51A Astrocyte

description: RNA-seq


title: P10_CD4_PD1low

description:
65_S49
Peripheral blood mononucleated cell

tag: diagnosis

tag: hbv dna [iu/ml]


title: SCZ_51C Astrocyte

description: RNA-seq


title: P24_CD4_PD1hi

description:
72_S54
Peripheral blood mononucleated cell

tag: hbsag [iu/ml]

tag: hbeag [pei u/ml]


title: P19_Bulk_CD8

description:
74_S55
Peripheral blood mononucleated cell

tag: cell type

tag: age


title: JK4_1_2_0_LT_4


title: P12_Bulk_CD8

description:
75_S56
Peripheral blood mononucleated cell

tag: hbv genotype


title: P16_CD4_PD1low

description:
69_S52
Peripheral blood mononucleated cell

tag: treatment


title: CLIP_GFP_R2

city: Santiago

first: Gino

last: Nardocci

address: Av. Mons. Álvaro del Portillo 12.455

country: Chile

institute: Universidad de los Andes

data_processing:
CLIP-seq reads were aligned to the hg38  using the Bowtie software (v2.1.1)
indexes were created using the BEDtools utilities (v2.24.0)
Peak finding  performed with Homer (v4.9). Three HMGN5 samples combined.   GFP2 and GFP3 samples as background
The number of reads per transcript was counted using HTSeq (v0.11.2)
Differentially expressed genes (DEGs) were estimated using SARTools (v1.6.9) and DEseq2 package from R (v1.24)
Genome_build: hg19
Supplementary_files_format_and_content: .txt files containing identified RNAs by Clip-seq

source_name: Fetal Kidney

growth_protocol: HMGN5-FlpIn cell lines were cultured in low glucose DMEM GlutaMAX™ supplemented with 10% Tetracycline-Free FBS (Biochrom), 100 µg/ml Hygromycin and 10 μg/ml Blasticidin, at 37°C and 5% CO2

extract_protocol:
Eluted RNA was purified from the beads using Trizol
Libraries were prepared using Ovation Universal RNA-seq kit (Nugen)

treatment_protocol: 70-80% confluent HMGN5-FlpIn cell line and GFP-FlpIn cell lines were induced 6h with 1µg/µl Doxycyclin, UV-crosslinked with 150 mJ/cm2 at 254nm and subjected to CLIP

tag: genotype

tag: plasmid transfected

value: TET induced

tag: cell line

value: Flp-In T-REx 293


title: P03_CD4_PD1low

description:
70_S53
Peripheral blood mononucleated cell

tag: cell number


title: SCZ_31C Astrocyte

description: RNA-seq

tag: disease


title: CLIP_HMGN5_R3


title: P09_Bulk_CD8

description:
67_S51
Peripheral blood mononucleated cell

tag: sample id

tag: patient id

value: Tenofovor

value: B


title: P08_CD4_PD1hi

description:
64_S48
Peripheral blood mononucleated cell

value: CD4 PD1+ T cells

tag: experiment day (facs run)

tag: sample number on experiment day

value: Tenofovir

value: <10 IU/mL


title: CLIP_HMGN5_R2


title: SCZ_52A Astrocyte

description: RNA-seq


title: SCZ_52B Astrocyte

description: RNA-seq


title: P05_Bulk_CD8

description:
66_S50
Peripheral blood mononucleated cell

tag: bleed date

tag: diagnosis

value: HV


title: P09_CD4_PD1low

description:
63_S47
Peripheral blood mononucleated cell

value: CD4 PD1- T cells

value: cHBV

tag: hbv dna [iu/ml]

tag: hbsag [iu/ml]


title: P04_Bulk_CD8

description:
61_S45
Peripheral blood mononucleated cell

tag: cell type

tag: hbeag [pei u/ml]


title: SCZ_51B Astrocyte

description: RNA-seq


title: P03_Bulk_CD8

description:
76_S57
Peripheral blood mononucleated cell

tag: age

tag: hbv genotype


title: CLIP_HMGN5_R1

tag: genotype


title: P06_CD4_PD1hi

description:
62_S46
Peripheral blood mononucleated cell

tag: treatment


title: SCZ_31B Astrocyte

description: RNA-seq


title: SCZ_31A Astrocyte

description: RNA-seq


title: CLIP_GFP_R1

tag: plasmid transfected

tag: cell line


title: P24_Bulk_CD8

description:
60_S44
Peripheral blood mononucleated cell

tag: cell number

value: rHBV


title: ChIP_HMGN5-R2

data_processing:
Raw sequencing reads were trimmed by removing Illumina adapters sequences and low-quality bases using Homer tools (v4.7)
ChiP-seq reads were aligned to  hg38 reference genome using Bowtie2 (v2.2.4)
Peak calling was performed using MACS2
peaks of individual replicates were combined in one peak file.
Genome_build: hg38
Supplementary_files_format_and_content: .txt files containing normalised  and annotated peaks

extract_protocol:
DNA  was isolated phenol/chloroform extraction
ChiP-Seq libraries were prepared using NEBNext® ChIP-Seq Library kit

treatment_protocol: Conditions used: HMGN5-FlpIn cell line  induced for 24h with (1µg/µl Doxycycline); uninduced HMGN5-FlpIn cells as background, and GFP-FlpIn control cell line. (70% confluent 10cm culture dish per replicate)


title: JK4_1_2_0_LT_8

tag: strain

value: BALB/c

tag: tissue

tag: timepoint


title: ChIP_HMGN5-R1


title: P13_CD4_PD1hi

description:
57_S41
Peripheral blood mononucleated cell

tag: sample id

tag: patient id

tag: experiment day (facs run)

tag: sample number on experiment day


title: P22_CD4_PD1hi

description:
56_S40
Peripheral blood mononucleated cell

tag: bleed date

tag: diagnosis

tag: hbv dna [iu/ml]

tag: hbsag [iu/ml]


title: P13_CD4_PD1low

description:
59_S43
Peripheral blood mononucleated cell

tag: cell type

tag: age

tag: hbeag [pei u/ml]

tag: hbv genotype


title: P08_HBV_core_18

description:
58_S42
Peripheral blood mononucleated cell

source_name: HBV_core_18  T cells

value: HBV_core_18  T cells

tag: treatment

value: D


title: ChIP_HMGN5+R2

tag: genotype

tag: plasmid transfected

tag: cell line


title: SCZ_164B Astrocyte

description: RNA-seq

tag: disease

value: schizophrenia


title: ChIP_HMGN5+R1


title: P19_CD4_PD1hi

description:
55_S39
Peripheral blood mononucleated cell

tag: cell number

tag: sample id


title: P16_Bulk_CD8

description:
52_S36
Peripheral blood mononucleated cell

value: Bulk CD8 T cells

tag: patient id

tag: experiment day (facs run)


title: ChIP_GFP+ control


title: P02_CD4_PD1hi

description:
54_S38
Peripheral blood mononucleated cell

tag: sample number on experiment day

tag: bleed date


title: P17_CD4_PD1low

description:
53_S37
Peripheral blood mononucleated cell

tag: diagnosis

tag: hbv dna [iu/ml]


title: CTR_C27D Astrocyte

description: RNA-seq

value: control


title: IPSCs, control, RNAseq, rep04

data_processing:
RNA-seq data were aligned to human reference genome (hg38) using hisat2 (v2.1.0).
The low-quality mapping reads (MAPQ < 20) were removed using ‘samtools view’ function of samtools (v1.3.1) and the remaining reads were sorted using ‘samtools sort’ function of samtools.
The coverage of sorted reads across the genome was calculated using ‘bamCoverage’ function of deepTools (v.3.4.3).
To quantify the gene transcription levels, we counted reads on exons of each gene using 'htseq-count' function of HTSeq (v0.11.2), utilizing human reference gene annotations download from Ensembl genome browser.
To exclude the impact of low or non-expressed genes on the analysis of differential expressed genes, we removed genes with cumulative reads count from all replicates less than 20. Differential expressed analysis was performed using DEseq2 (1.30.1) R package with thresholds '|log2(fold change)|>1 and FDR<0.05'.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for all samples.

source_name: Peripheral blood

extract_protocol:
Total RNA was extracted using RNAiso Plus solution (Takara Bio Inc., Japan). 1 ug total RNA was used for the construction of sequencing libraries.
Total RNA was quality and quantity were detected using Nanodrop 2000 (Thermo Fisher Scientific, MA, USA) as well as Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA). The mRNA was enriched from qualified samples using Oligo (dT) coated beads and then was fragmented using fragmentation buffer. The RNA fragments were reverse transcribed to synthesize cDNA using random primers. The library was prepared through sequentially end repair, A-Tailing, adapter ligation, size selection, and amplification.

tag: tissue

value: Peripheral blood

tag: cell type

value: IPSCs

value: Normal


title: CTR_C27C Astrocyte

description: RNA-seq


title: P17_Bulk_CD8

description:
50_S34
Peripheral blood mononucleated cell

tag: age

tag: hbsag [iu/ml]

tag: hbeag [pei u/ml]


title: CTR_C27B Astrocyte

description: RNA-seq


title: CTR_C27A Astrocyte

description: RNA-seq


title: P21_Bulk_CD8

description:
48_S32
Peripheral blood mononucleated cell

tag: treatment

tag: hbv genotype


title: P23_CD4_PD1hi

description:
47_S31
Peripheral blood mononucleated cell


title: P18_CD4_PD1low

description:
46_S30
Peripheral blood mononucleated cell


title: P25_CD4_PD1low

description:
51_S35
Peripheral blood mononucleated cell


title: IPSCs, control, RNAseq, rep03

tag: genotype


title: CTR_22D Astrocyte

description: RNA-seq

tag: disease


title: IPSCs, control, RNAseq, rep02


title: P21_CD4_PD1hi

description:
45_S29
Peripheral blood mononucleated cell

tag: cell number


title: IPSCs, control, RNAseq, rep01


title: SCZ_164D Astrocyte

description: RNA-seq


title: CTR_22C Astrocyte

description: RNA-seq


title: P09_CD4_PD1hi

description:
43_S27
Peripheral blood mononucleated cell

tag: sample id

value: Tenofovor

value: B


title: IPSCs, patient, RNAseq, rep05


title: P03_CD4_PD1hi

description:
44_S28
Peripheral blood mononucleated cell

value: CD4 PD1+ T cells

tag: patient id


title: P25_CD4_PD1hi

description:
41_S26
Peripheral blood mononucleated cell

tag: experiment day (facs run)

value: <10 IU/mL


title: CTR_22B Astrocyte

description: RNA-seq


title: P04_CD4_PD1low

description:
40_S25
Peripheral blood mononucleated cell

tag: sample number on experiment day

value: HV


title: IPSCs, patient, RNAseq, rep04


title: P11_CD4_PD1low

description:
37_S23
Peripheral blood mononucleated cell

value: CD4 PD1- T cells

tag: bleed date

value: A


title: P14_CD4_PD1low

description:
39_S24
Peripheral blood mononucleated cell

tag: diagnosis

value: cHBV


title: P08_Bulk_CD8

description:
49_S33
Peripheral blood mononucleated cell

value: Tenofovir

tag: hbv dna [iu/ml]


title: CTR_208C Astrocyte

description: RNA-seq


title: P06_CD4_PD1low

description:
36_S22
Peripheral blood mononucleated cell


title: IPSCs, patient, RNAseq, rep02

tag: tissue


title: P20_CD4_PD1hi

description:
35_S21
Peripheral blood mononucleated cell

tag: cell type

value: rHBV


title: CTR_208A Astrocyte

description: RNA-seq


title: IPSCs, patient, RNAseq, rep01


title: P20_Bulk_CD8

description:
34_S20
Peripheral blood mononucleated cell

tag: age


title: CTR_205C Astrocyte

description: RNA-seq


title: P13_Bulk_CD8

description:
33_S19
Peripheral blood mononucleated cell

tag: hbsag [iu/ml]


title: 5C_YUCHIME [RPPA]

type: protein

city: New York

first: Tiphaine

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute

hyb_protocol: Serially diluted cellular proteins are arrayed on nitrocellulose‐coated slides and probed with validated antibodies that recognize signaling molecules in their functional state. Signals are captured by tyramide dye deposition and a DAB colorimetric reaction. 200 ng RNA was hybridized to a custom NanoString panel code set according to the recommendations of the manufacturer (NanoString Technologies, Inc., Seattle, Washington, USA).

scan_protocol: Data is collected and quantitative analysis is performed using custom “Supercurve”software developed for this purpose. The values derived from the slope and intercept  are expressed relative to standard control cell lysates or control peptides on the array. Thesevalues indicate the levels of protein expression and modification (phosphorylation or cleavage based on antibody specificity) Following hybridization, the target-probe complexes were purified and immobilized on the nCounter prep station. Digital counts for each gene-specific target RNA were then acquired on the nCounter detection analyzer and normalized to account for differences in tissue mRNA quantity as well as slight differences in assay efficiency.

data_processing:
Each dilution curve was fitted with a logistic model (“Supercurve Fitting” developed by the Department of Bioinformatics and Computational Biology in MD Anderson Cancer Center, “http://bioinformatics.mdanderson.org/OOMPA”). This fits a single curve using all the samples (i.e., dilution series) on a slide with the signal intensity as the response variable and the dilution steps are independent variable. The fitted curve is plotted with the signal intensities – both observed and fitted ‐ on the y‐axis and the log2‐concentration of proteins on the x‐axis for diagnostic purposes. The protein concentrations of each set of slides were then normalized for protein loading. Correction factor was calculated by: 1) median‐centering across samples of all antibody experiments; and 2) median‐centering across antibodies for each sample.
The nSolver analysis software version 4.0 (NanoString Technologies) was used for extraction of raw digital counts of expression, checking the quality of the data, normalizing expression values using housekeeping genes, and generating heatmaps.

molecule: protein

source_name: melanoma cell line_YUCHIME

label_protocol:
NA
Specimens were labeled with decode assignment which was linked to tumor origin.

growth_protocol:
This cohort includes human cell lines (n=5, in triplicate). WM35, WM983, and WM1552c were grown in 2% tumor media containing a 4:1 mixture of MCDB 153 medium with 1.5 g/L sodium bicarbonate and Leibovitz's L-15 medium with 2 mM L-glutamine supplemented with 0.005 mg/ml bovine insulin, 1.68 mM CaCl2, and 2% fetal bovine serum. . YUPEET and YUCHIME were grown in bFGF media (OPTIMEM, 5% FBS, 10ng/ml bFGF, 1ng/ml heparin, 0.1mM dbcAMP, 0.1mM IBMX.)
This cohort includes human tissue obtained from FFPE (n=205), fresh frozen human tissue (n=24), and human cell lines (n=12).

extract_protocol:
Cell were lysed using lysis Buffer (1% Triton X‐100, 50mM HEPES, pH 7.4, 150mM NaCl, 1.5mM MgCl2, 1mM EGTA, 100mM NaF, 10mM Na pyrophosphate, 1mM Na3VO4, 10% glycerol, containing freshly added protease and phosphatase inhibitors) for 30 minutes while shaking. The cell lysates were centrifuged at 14,000 rpm for 10 minutes at 4C. Supernatant was collected, pellet discarded. Protein concentration was quantified by Qubit and adjusted to 1.5 ug/ul. (using lysis buffer to dilute). The cell lysate was mixed with (4XSDS + B‐Me) sample buffer without bromophenol blue (3 parts of cell lysate plus one part of 4XSDS sample buffer). The samples were boiled for 5 minutes, and stored in –80C until sample submission.
RNA was obtained from the FFPE human tissue samples using the RecoverAll Total Nucleic Acid Isolation kit. RNA was obtained from the fresh frozen human tissue samples using the Qiagen Rneasy kit. Cell lines were pelleted and RNA was harvested using the Qiagen Rneasy kit.

treatment_protocol:
N/A
None

tag: gender

value: M

tag: age at diagnosis

tag: cohort

value: Yale

value: primary cutaneous melanoma tissue


title: CTR_205B Astrocyte

description: RNA-seq

value: control


title: Control

data_processing:
Raw sequencing reads were trimmed by removing Illumina adapters sequences and low-quality bases
pre-processing steps were performed using the SAMtools or BEDtools packages
Trimmed reads were mapped using STAR software
The number of reads per transcript was counted using HTSeq (v0.11.2)
The differentially expressed genes (DEGs) were estimated using DEseq2 package from R (v3.1.2)
Genome_build: hg19
Supplementary_files_format_and_content: .txt files containing normalised counts and differential expression analysis data (DESeq2)

extract_protocol:
RNA  was extracted with the NucleoSpin RNA Kit (MACHEREY-NAGEL)
Libraries were prepared using TruSeq RNA Sample Preparation Kit v2

treatment_protocol: 3 conditions were used 70-80% confluent HMGN5-FlpIn cell line were induced 24h with (1µg/µl Doxycycline); 24h HMGN5 knock-down (40 nM of a SmartPool siRNA) and  non-treated control cells (70% confluent 10cm culture dish per replicate)

tag: genotype

tag: plasmid transfected

tag: cell line

value: Flp-In T-REx 293


title: 5B_YUCHIME [RPPA]


title: P02_Bulk_CD8

description:
32_S18
Peripheral blood mononucleated cell

value: Bulk CD8 T cells

tag: cell number

tag: sample id

tag: treatment

tag: hbeag [pei u/ml]

tag: hbv genotype


title: knockdown

value: non_induced/siRNA HMGN5


title: 5A_YUCHIME [RPPA]


title: IPSCs, patient, RNAseq, rep03

value: Peripheral blood

value: IPSCs


title: 4C_WM1552C [RPPA]

source_name: melanoma cell line_WM1552C

value: Wistar


title: CTR_19C Astrocyte

description: RNA-seq

tag: disease


title: P01_Bulk_CD8

description:
30_S16
Peripheral blood mononucleated cell

tag: patient id

tag: experiment day (facs run)

tag: sample number on experiment day

tag: bleed date

tag: diagnosis

tag: hbv dna [iu/ml]


title: P25_Bulk_CD8

description:
31_S17
Peripheral blood mononucleated cell

tag: cell type

tag: age

value: <10 IU/mL

tag: hbsag [iu/ml]


title: OverExpression

tag: genotype

tag: plasmid transfected

value: TET induced


title: T47D cells, Progesterone vehicle 3

city: Laval

first: Isabelle

last: Plante

state: Québec

address: 531 boul Des prairies

department: Armand-Frappier Santé Biotechnologie

country: Canada

institute: INRS

description:
PV3
norm_counts_limmaremovebatch_progesterone

library_source: other

data_processing:
The quality of the raw reads was assessed with FASTQC v0.11.8. Reads were trimmed using Cutadapt keeping the 22 first nucleotides. Micro-RNA were quantified using MIRDEEP software. Other small RNA were quantified using COMPSRA. Results were aggregate as a matrix and used as input into DESeq2 R package for differential expression. Differential expression was performed for all comparisons within each hormone separately while controlling for batch effect in the model.
Assembly: hg38
Supplementary files format and content: Excel sheets represent normalized counts.

molecule: other

source_name: Breast

extract_protocol:
mirVana miRNA isolation kit (Thermo Fisher Scientific).
libraryTruseq Small RNA

tag: tissue

value: Breast

tag: cell line

value: 0.1% ethanol


title: P02_CD4_PD1low

description:
29_S15
Peripheral blood mononucleated cell

value: CD4 PD1- T cells

tag: cell number

tag: sample id

value: HV

tag: treatment


title: T47D cells, Progesterone vehicle 2

description:
PV2
norm_counts_limmaremovebatch_progesterone


title: CTR_19B Astrocyte

first: Steven

institute: University of Rochester Medical Center

description: RNA-seq

tag: disease


title: CTR_22A Astrocyte

description: RNA-seq


title: CTR_17C Astrocyte

description: RNA-seq


title: T47D cells, Progesterone vehicle 1

description:
PV1
norm_counts_limmaremovebatch_progesterone


title: 4B_WM1552C [RPPA]

tag: gender

tag: age at diagnosis

tag: cohort


title: P16_CD4_PD1hi

description:
26_S13
Peripheral blood mononucleated cell

value: CD4 PD1+ T cells

tag: patient id

tag: experiment day (facs run)

tag: sample number on experiment day

tag: bleed date

value: rHBV

tag: hbeag [pei u/ml]

tag: hbv genotype


title: P19_CD4_PD1low

description:
28_S14
Peripheral blood mononucleated cell

tag: cell type

tag: age

tag: diagnosis

tag: hbv dna [iu/ml]

tag: hbsag [iu/ml]


title: 4A_WM1552C [RPPA]

value: M


title: CTR_19A Astrocyte

description: RNA-seq


title: T47D cells, Progesterone treated 3

description:
PT3
norm_counts_limmaremovebatch_progesterone

tag: tissue

tag: cell line

value: Progesterone 10 nM, 6 hours


title: 3B_WM983 [RPPA]

source_name: melanoma cell line_WM793

value: primary cutaneous melanoma tissue


title: CTR_17A Astrocyte

description: RNA-seq

tag: disease

value: control


title: CTR_17B Astrocyte

description: RNA-seq


title: 3C_WM983 [RPPA]

tag: gender


title: T47D cells, Progesterone treated 2

description:
PT2
norm_counts_limmaremovebatch_progesterone

tag: treatment


title: P23_Bulk_CD8

description:
25_S12
Peripheral blood mononucleated cell

value: Bulk CD8 T cells

tag: cell number

tag: sample id


title: P04_CD4_PD1hi

description:
24_S11
Peripheral blood mononucleated cell

tag: patient id

tag: experiment day (facs run)


title: SCZ_52F GPC

description: RNA-seq

source_name: GPC induced from iPSC

value: schizophrenia


title: 3A_WM983 [RPPA]

tag: age at diagnosis

tag: cohort


title: T47D cells, Progesterone treated 1

description:
PT1
norm_counts_limmaremovebatch_progesterone


title: 2C_YUPEET [RPPA]

source_name: melanoma cell line_YUPEET

value: Yale


title: P10_CD4_PD1hi

description:
23_S10
Peripheral blood mononucleated cell

tag: sample number on experiment day

tag: bleed date

value: cHBV

value: Viread

tag: hbeag [pei u/ml]

tag: hbv genotype


title: SCZ_52E GPC

description: RNA-seq


title: T47D cells, Progesterone control 3

description:
PC3
norm_counts_limmaremovebatch_progesterone


title: 2B_YUPEET [RPPA]

tag: cell type


title: P10_Bulk_CD8

description:
22_S9
Peripheral blood mononucleated cell

tag: age

tag: diagnosis

tag: hbv dna [iu/ml]

value: <10 IU/mL

tag: hbsag [iu/ml]


title: T47D cells, Progesterone control 2

description:
PC2
norm_counts_limmaremovebatch_progesterone

tag: tissue

tag: cell line


title: SCZ_52D GPC

description: RNA-seq

tag: disease


title: SCZ_52C GPC

description: RNA-seq


title: 2A_YUPEET [RPPA]

tag: gender


title: P24_CD4_PD1low

description:
21_S8
Peripheral blood mononucleated cell

tag: cell number

tag: sample id

tag: patient id

tag: treatment


title: P07_CD4_PD1low

description:
19_S7
Peripheral blood mononucleated cell

tag: experiment day (facs run)

tag: sample number on experiment day

value: D


title: SCZ_52B GPC

description: RNA-seq


title: 1C_WM35 [RPPA]

source_name: melanoma cell line_WM35

value: F

tag: age at diagnosis

tag: cohort

value: Wistar


title: P12_CD4_PD1hi

description:
17_S6
Peripheral blood mononucleated cell

tag: cell type

tag: bleed date

tag: hbeag [pei u/ml]

tag: hbv genotype


title: SCZ_52A GPC

description: RNA-seq


title: T47D cells, Oxytocin vehicle 2

description:
OV2
norm_counts_limmaremovebatch_oxytocin

value: Breast

value: water


title: SCZ_31D GPC

description: RNA-seq


title: P01_CD4_PD1low

description:
16_S5
Peripheral blood mononucleated cell

value: CD4 PD1- T cells

tag: age

tag: diagnosis

value: HV

tag: hbv dna [iu/ml]

tag: hbsag [iu/ml]


title: Myco Feriruminatoris 1_b

city: Barcelona

first: Ludovica

last: Ciampi

state: Choose a State or Province

address: Carrer del Doctor Aiguader 88

country: Spain

institute: Centre for Genomic Regulation

data_processing:
Alignment to the reference genome using bowtie2 v. 2.3.5
SAM to BAM convertion using using samtools v. 1.9
Fragment counts per annotation region were computed using bedtools
Strand-specific per-base coverage was computed using bedtools
Assembly: NZ_CP091032.1
Supplementary files format and content: Files with raw read count and Transcripts per million (TPM) based on fragment count

organism: Mycoplasma feriruminatoris

source_name: mycoplasma

growth_protocol: Grown in suspension at 37˚C in Hayflick media until exponential phase.

extract_protocol:
Cells separated from supernatant by centrifugation at 10,000 rpm and washed 3 times in PBS 1x. Bacterial pellet treated with RLT buffer (Rneasy kit, Qiagen) supplemented with 1:100 beta-mercaptoethanol. The rest of the protocol was followed as per the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
polyA-selected stranded RNA-seq

treatment_protocol: The cultures were untreated while growing.

value: mycoplasma

tag: genotype

value: WT

value: Untreated


title: T47D cells, Oxytocin vehicle 1

description:
OV1
norm_counts_limmaremovebatch_oxytocin

tag: tissue

tag: cell line


title: 1A_WM35 [RPPA]

last: Martin

tag: gender

value: primary cutaneous melanoma tissue


title: Myco Feriruminatoris 1_a

tag: treatment


title: P11_Bulk_CD8

description:
14_S4
Peripheral blood mononucleated cell

value: Bulk CD8 T cells

tag: cell number

tag: sample id

tag: patient id

tag: experiment day (facs run)

value: A


title: T47D cells, Oxytocin treated 3

description:
OT3
norm_counts_limmaremovebatch_oxytocin

value: Oxytocin 100 nM,  24 hours


title: Mtb infected MAEA knockdown macrophages 4 days post infection_3

city: Ithaca

first: Nelson

middle: Victor

last: Simwela

address: 930 Campus Rd

department: Microbiology and Immunology

institute: Cornell University

data_processing:
STAR-2.7.10b
Reads were mapped to GRCm39 and ASM19595v2 using STAR. Raw read counts were obtained from mapped reads using HTSeq count
Raw and normalised reads were analyzed using DESeq2
Assembly: mm10, ASM19595v2
Supplementary files format and content: txt files for both raw and normalized counts

organism:
Mycobacterium tuberculosis
Mus musculus

source_name: Bone marrow macrophages

extract_protocol:
RNA was extracted using TRIZOL, total RNA from the aqueous phase was purified using the Zymo RNA clean and concentrator kit
Barcoded RNAseq libraries were generated with the NEBNext Ultra II [Directional] RNA Library Prep Kit after ribosomal rRNA depletion using the QIAseq FastSelect pan-bacterial and H/M/R kits
Novaseq 6000 S4

tag: cell type

value: Bone marrow macrophages

value: MAEA knockdown

tag: infection

value: Mtb infected - 4 days


title: P14_Bulk_CD8

description:
13_S3
Peripheral blood mononucleated cell

tag: sample number on experiment day

tag: bleed date

value: cHBV

tag: hbeag [pei u/ml]

value: D


title: T47D cells, Oxytocin treated 2

description:
OT2
norm_counts_limmaremovebatch_oxytocin


title: Mtb infected MAEA knockdown macrophages 4 days post infection_2


title: SCZ_31B GPC

city: Rochester

address: 601 Elmwood Ave

description: RNA-seq

tag: disease

value: schizophrenia


title: SCZ_31A GPC

description: RNA-seq


title: T47D cells, Progesterone control 1

description:
PC1
norm_counts_limmaremovebatch_progesterone

value: Breast


title: P07_CD4_PD1hi

description:
12_S2
Peripheral blood mononucleated cell

value: CD4 PD1+ T cells

tag: age

tag: diagnosis

value: Viread

tag: hbv dna [iu/ml]

value: <10 IU/mL

tag: hbv genotype


title: Mtb infected MAEA knockdown macrophages 4 days post infection_1

tag: genotype


title: T47D cells, Oxytocin treated 1

description:
OT1
norm_counts_limmaremovebatch_oxytocin

tag: tissue

tag: cell line


title: CTR_C27F GPC

description: RNA-seq

value: control


title: 1B_WM35 [RPPA]

tag: gender

value: F

tag: age at diagnosis

tag: cohort

value: Wistar


title: T47D cells, Oxytocin control 3

description:
OC3
norm_counts_limmaremovebatch_oxytocin

tag: treatment


title: T47D cells, Oxytocin vehicle 3

description:
OV3
norm_counts_limmaremovebatch_oxytocin

value: water


title: Mtb infected WDR26 knockdown macrophages 4 days post infection_3

tag: cell type

value: WDR26 knockdown


title: P18_Bulk_CD8

description:
11_S1
Peripheral blood mononucleated cell

value: Bulk CD8 T cells

tag: cell number

tag: sample id

tag: patient id

tag: experiment day (facs run)

value: rHBV

tag: hbsag [iu/ml]


title: Mtb infected WDR26 knockdown macrophages 4 days post infection_2

value: Bone marrow macrophages

tag: infection


title: A375_siGL2-pQ_R3

city: Lyon

first: Nicolas

last: Fontrodona

address: 46 allée d'Italie

country: France

institute: ENS de Lyon

data_processing:
Adapters were removed from raw reads and trimmed using fastp version 0.20.1 (parameters --qualified_quality_phred 30 -l 25 --detect_adapter_for_pe)
Reads were mapped against the human genome GRCh38.p13 with hisat2 version 2.2.1
Reads were counted with htseq-count version 0.13.5. (parameters -r pos -a 10 -s reverse -t exon).
Assembly: GRCH38.p13
Supplementary files format and content: tab-delimited text file containing raw read counts for each sample. (readcounts_raw_44659genes.csv)

molecule: cytoplasmic RNA

growth_protocol: A375 cells were obtained from ATCC and cultured in DMEM containing all amino-acids except glutamine (Gibco, 10938025) and supplemented with 10% FBS, 2mM glutamine and penicillin-streptomycin, at 37°C and 5% CO2. Cells were passed at around 80% confluency, 3 times a week.

extract_protocol:
Cells were washed twice with ice cold PBS, then scrapped with 1ml of PBS. Then they were centrifuged (500g for 1min at 4°C) and slowly resuspended in 1ml of lysis buffer (10mM Tris-HCL pH7.5; 5mM MgCl2; 100 mM KCl; 1% Triton X-100), and incubated on ice for 10 minutes. After this, lysates were centrifuged (1000g for 10minutes at 4°C), and RNAs were extracted from cytoplasmic fractions using tri-reagent (Sigma, T9424) following the manufacturer’s instructions.
RNA samples were sent for sequencing at Novogene (rRNA depletion library preparations, sequencing on Novaseq 6000 2x150)

treatment_protocol:
Transfection : For each gene of interest (except for GL2), 2 different siRNAs targetting constitutive exons and with minimum predicted off-targets were designed and pooled together. siRNAs were ordered lyophilysed from Merck and resuspended in sterile water at 50µM, and stored at -20°C. Cells were reverse-transfected with lipofectamine RNAimax (Thermofischer 13778030) according to the manufacturer’s instructions.
24h later, medium was removed and cells washed with warm PBS and a new medium containing (MAPK inhibitors or DMSO) OR (glutamine or not) was used, and cells harvested 24h later.

value: skin melanoma

value: control medium + siGL2


title: CTR_C27E GPC

last: Goldman

description: RNA-seq

tag: disease


title: T47D cells, Oxytocin control 2

description:
OC2
norm_counts_limmaremovebatch_oxytocin


title: A375_siGL2-pQ_R2


title: T47D cells, Oxytocin control 1

description:
OC1
norm_counts_limmaremovebatch_oxytocin


title: SCZ_31C GPC

description: RNA-seq


title: CTR_C27D GPC

description: RNA-seq


title: CTR_C27C GPC

description: RNA-seq


title: A375_siGL2-pQ_R1


title: T47D cells, Estradiol vehicle 3

description:
EV3
norm_counts_limmaremovebatch_estradiol

value: 0.1% ethanol


title: CTR_C27B GPC

description: RNA-seq


title: Mtb infected GID8 knockdown macrophages 4 days post infection_2

value: GID8 knockdown

value: Mtb infected - 4 days


title: CTR_C27A GPC

description: RNA-seq


title: T47D cells, Estradiol vehicle 2

description:
EV2
norm_counts_limmaremovebatch_estradiol

value: Breast


title: A375_siGL2-mQ_R2

value: Q depleted medium + siGL2


title: T47D cells, Estradiol vehicle 1

description:
EV1
norm_counts_limmaremovebatch_estradiol


title: Mtb infected GID8 knockdown macrophages 4 days post infection_1


title: CTR_22H GPC

description: RNA-seq


title: A375_siGL2-mQ_R1


title: T47D cells, Estradiol treated 3

description:
ET3
norm_counts_limmaremovebatch_estradiol

value: Estradiol 10 nM,  24 hours


title: CTR_22G GPC

description: RNA-seq


title: A375_siGL2-MAPKi_R3

value: MAPK inhibitors + siGL2


title: Mtb infected Scramble sgRNA macrophages 4 days post infection_2

value: Scramble (WT)


title: T47D cells, Estradiol treated 2

description:
ET2
norm_counts_limmaremovebatch_estradiol


title: Mtb infected Scramble sgRNA macrophages 4 days post infection_3


title: Mtb infected WDR26 knockdown macrophages 4 days post infection_1


title: A375_siGL2-MAPKi_R2


title: Mtb infected Scramble sgRNA macrophages 4 days post infection_1


title: A375_siGL2-MAPKi_R1


title: T47D cells, Estradiol control 2

description:
EC2
norm_counts_limmaremovebatch_estradiol


title: T47D cells, Estradiol control 3

description:
EC3
norm_counts_limmaremovebatch_estradiol


title: A375_siGL2-DMSO_R3

value: DMSO + siGL2